You Belong To Me
by ShaViva
Summary: "Am I the only one worried about you?" Rodney asked. Sheppard's deepening connection to Atlantis offers unexpected solutions when a threat from within risks the safety of everyone in the city. Sequel 2 Feelin' Hot Hot Hot. Sheplantis, Shep whump
1. Remember, we don't want to turn it on

**You belong to me**

Author: ShaViva

Rating: T

Content Warning: Some action violence, a couple of instances of language, rated T to be safe

Season: Season 3, after 'McKay and Mrs Miller' and before 'The Return Part 1'

Summary: "Am I the only one worried about you?" Rodney asked. Sheppard's deepening connection to Atlantis offers unexpected solutions when a threat from within risks the safety of everyone in the city. Shep Whump plus Sheplantis. Also lots of team friendship, especially Shep/McKay friendship.

Classifications: Adventure, Drama, Team Friendship

Pairings: None

Spoilers for: Nothing really – minor references to 'Common Ground' and 'McKay and Mrs Miller'.

Disclaimer: The Stargate characters, storylines, etc aren't mine – I'm just playing with them for my own, and hopefully _your_ enjoyment. I am unfortunately not associated in any way with the creators, owners, or producers of Stargate or any of its media franchises. All publicly recognizable characters, settings, equipment, etc are the property of whoever owns them. Any original characters and plot and anything else I made up are the property of me, the author. No copyright infringement is intended.

Copyright (c) 2008 ShaViva

**Authors Note:**

This story follows on from "Feelin' Hot Hot Hot". You can probably work most things out if you haven't read Hot Hot Hot and you can't be bothered going and doing it now ... so don't let that stop you from reading on. I mean I'd like it if you did go and read Hot Hot Hot ... but you don't have to :D

On with the new story ...

**Chapter 1: Remember, we don't want to turn it on**

Lt Colonel John Sheppard rubbed a tired hand over his face, propping his feet on his desk as he tried to finish reading the background information Rodney had prepared for their next mission briefing the following morning. It was already late evening and he really needed to get it done so he could get some much needed sleep.

"Sheppard," Doctor Rodney McKay's voice issued from Sheppard's radio ear piece. "I need you down here in the lab."

"Can't it wait McKay?" Sheppard replied irritably. "I'm still wading through your War and Peace on the mission to M4R-993."

"No it can't wait!" Rodney exclaimed impatiently. "We've discovered a new system within the database and I need your ... help working out what it is."

"Oh," Sheppard frowned, knowing that Rodney was alluding to having him use his unique connection with Atlantis to find out more information. "Fine ... I'll be there in a few minutes."

It had only been a couple of weeks since John had discovered he even had the ability to find out things by directly talking with the city. The whole idea still freaked him out a bit and he wasn't sure he was ready to open that door again so soon. Sure he still heard the city humming in his head, still felt that warm tingle under the skin. After more than two years he'd become accustomed to it, to the point where he hardly noticed it. That was still the case now that those things had become stronger, more insistent.

In the end Sheppard _had_ agreed with Rodney that controlled access to information they couldn't have gotten otherwise was an advantage they had to use. Translation – he had to force himself to access a part of himself he really wasn't comfortable with.

"Don't you ever sleep McKay?" Sheppard greeted Rodney as he strode into the lab. Glancing around he noticed immediately that Rodney had already given his two underlings still on duty tasks that took them outside of hearing range.

"When I have to," Rodney dismissed the comment, motioning Sheppard over to his workspace.

"What have you got?" Sheppard looked curiously over Rodney's shoulder.

"Not sure," Rodney admitted, drawing Sheppard's attention to some diagrams on his laptop screen. They looked like schematics for some kind of cube like structure with lots of pathways travelling in many directions. "Doctor Spencer came across this system while running a new cross referencing program on the Ancient database."

"Who's Spencer again?" Sheppard tried to remember where all the scientists slotted in but some of them he only came into contact with infrequently, if at all.

"He's our resident systems architecture expert,' Rodney replied, waving his hand to indicate Spencer's specialty wasn't relevant to the discussion. "The important thing is that the design of the system suggests the Ancients deliberately segregated it away from all the other systems. It's substantial but it looks like it hasn't been activated probably since they abandoned the city."

"And why do we care?" Sheppard raised an eyebrow expectantly.

"Because without a ZedPM we need every advantage we can get," Rodney said in his 'isn't it obvious' tone. "Look, this could be some kind of defensive system to supplement the shields, or a ... a new power control system or -"

"Or a program to keep track of the local football tipping competition," Sheppard broke in to suggest snidely.

"Can you just ask Atlantis what the system does please?" Rodney asked with a long suffering sigh.

"Have you tried to work out what it is on your own?" Sheppard turned serious, considering the problem from all angles. "You know I'm not keen for us to rely on Atlantis when we have the means to solve problems ourselves."

"I already tried accessing the system from the main lab console," Rodney said impatiently. "I couldn't get in. Doctor Cooper did a search of the database too and didn't find squat."

"Fine," Sheppard walked over to the control console himself. "Let's just see if I can access the system first. If I can't, then we'll ask Atlantis."

"Remember, we don't want to turn it on," Rodney coached, looking on with a faintly worried expression. "Just lean on it a little so we can find out what it's for."

"I _have_ done this just a few times before McKay," Sheppard drawled, putting his hands on the science console and directing his attention to the system Rodney had called up for access. Concentrating hard, Sheppard thought 'overview', looking for a rundown on the system purpose and specifications. Nothing happened so he leaned just a little firmer, sending the same thought. The air pulsed ... like a ripple of energy shimmering through everything as it travelled from ceiling to floor.

"Crap, what was that?" John turned to glance at Rodney in concern, skin tingling slightly.

"What was what?" Rodney asked in confusion, looking over Sheppard's shoulder as if whatever was on the console would be able to explain the question.

"That ... pulse," Sheppard persisted, still feeling somewhat disorientated. "Didn't you feel it?"

"No," Rodney denied with a frown. "Is it still there?"

"Ah ... no. I'm not picking up anything," Sheppard stood still for a moment waiting for something to happen before shrugging. "There's nothing coming from this console either."

"So can we ask Atlantis for help now?" Rodney looked at Sheppard hopefully.

"Sure," Sheppard agreed, closing his eyes to have a little conversation in his head. "_You there?_" he called out softly, expecting the usual immediate response. None was forthcoming. "_Hello? Atlantis?_" Still nothing. Opening his eyes Sheppard looked at Rodney in puzzlement. "I'm not getting anything."

"Atlantis can't help?" Rodney asked incredulously.

"No Rodney," Sheppard countered. "I'm not getting anything from Atlantis ... she's just not there."

"What, nothing at all?" Rodney responded weakly.

"No words, no hum, no familiar tingle under the skin," Sheppard confirmed. "Nothing at all."

"We are in so much trouble," Rodney said in a panicky tone.

TBC


	2. You're actually hoping it's gone

**Chapter 2: You're actually hoping it's gone, aren't you?**

"It's not like we can just go to Elizabeth and tell her something's wrong with Atlantis," Sheppard argued with Rodney's immediate desire to suspect the worst and act accordingly.

"We could," Rodney muttered, "if you were willing to give up the 'I'm just like the rest of you' routine and tell her the full story."

"Do you want me to get shipped off to Area 51?" Sheppard demanded harshly, hardly aware that his raised voice was starting to draw attention from across the room.

"No," Rodney replied heatedly, "of course not ... but aren't you the least bit concerned that something might be wrong?"

"Everything else is working isn't it?" Sheppard asked, pretty sure the answer was yes since the lights were still on and no one had radioed Rodney in a panic yet.

"As far as I can tell," Rodney admitted, "but that doesn't mean anything!"

"It's just as likely that something's switched off in _my_ head," Sheppard pointed out. "Just because I can't hear the city anymore doesn't mean there's something wrong in the systems. Maybe Atlantis just went on vacation."

"Oh that's just like you isn't it," Rodney complained. "Why can't you be serious instead of turning everything into a joke?!"

"You take everything seriously enough for the both of us," Sheppard pointed out casually.

"_Of course!_" Rodney exclaimed with dawning understanding. "You're glad about this! You never wanted to have this connection and you're actually hoping it's gone, aren't you?"

"Let's not assume anything," Sheppard deliberately ignored Rodney's question. "In any case now's not the time to talk about this," he glanced pointedly at Rodney's staff, noticing finally that they were watching him and Rodney with more than just a passing interest.

Rodney looked up, face telling its own story that he'd forgotten anyone else was in the lab. "If you've got time to watch us you've got time to finish those analysis reports," Rodney dished out the punishment, scowling at the offenders until they guiltily bent back to their work.

"Run a full system diagnostic," Sheppard suggested. "If that comes back clean we'll work out what we want to do next."

Not waiting for Rodney to start grumbling, Sheppard strode out the door and back to his own office. Trying to get his mind back on the mission briefing proved impossible ... unrelated thoughts were running through his head and he just couldn't concentrate on reading Rodney's overly verbose report. He'd felt tired _before_ heading down to Rodney's lab - now he was finding it hard to keep his eyes open.

Thinking he'd just have to finish the report before the meeting tomorrow, Sheppard walked wearily back to his quarters and immediately stretched out on his bed. Now that he was alone he admitted to himself how torn he was about what had happened in the lab. On the one hand he was glad to have one less thing to worry about ... the fear of discovery had been playing at the back of his mind since the hydrothermal vent had first begun to affect the city. But if he was honest he'd have to admit that it was too quiet ... he'd become used to the constant company, in his head and across his skin, and now the lack of that was just as disturbing as the presence of it had been when he'd first arrived. Shaking his head at the contradiction, Sheppard turned over and buried his head in his pillow. Within moments he'd dropped into a deep sleep.

x

"_Take your fill," Kolya ordered. The Wraith slammed a hand down on John's chest, howling rapaciously as it slowly sucked the life from him. Sheppard felt the skin shrivelling over his entire body, writhing in agony at a million imaginary claws scratching at his arms, his face, everywhere. Added to that was the nightmare feeling of being eaten alive from the inside by tiny unnamed predators who delighted in drinking the very moisture from his blood. His scalp tightened painfully as dark hair that had been thick and full of character thinned and turned grey and then white. And still the agony went on until it became his whole world, unending, without purpose. _

_Sheppard retained just enough awareness to look beyond the Wraith to the man who'd captured him and perpetrated this atrocity. His stomach roiled as Kolya grinned at him, delighted to observe the feeding, viciously enjoying the sight of Sheppard's life slowing being stolen away. "Finish it!" Kolya's voice rang with evil pleasure. The Wraith howled again, taunting Sheppard with its malevolent hiss and flick of head. The pain intensified to a point Sheppard was sure meant death was only seconds away ..._

x

John jerked up in his bed, covered in sweat and panting harshly. Bringing up shaking hands he covered his face, almost moaning at the harshness of the images that had assaulted his dreams. "Jesus where did that come from?!" he muttered aloud. Dreams about past events were pretty common place, but not like that, and not so removed from the reality of what had actually happened.

Concentrating on deep even breathing Sheppard slowly brought himself back under control. Walking to his bathroom he glanced in the mirror, grimacing at the pale, troubled image that gazed back. Splashing water on his face and drying off quickly, Sheppard finished in the bathroom, carefully avoiding looking at himself again. Settling back into bed, he lay stretched out gazing up at the ceiling. He didn't think it possible but moments later he dropped back into sleep.

x

"_You did not think I would really help you to escape?" the Wraith prisoner sneered gleefully at Sheppard's crestfallen expression. "You did! You humans are truly pathetic." The Wraith took deliberate steps towards him and Sheppard knew another feeding was probably unavoidable. Still he turned and hobbled off into the trees, puffing and wheezing like the old man he'd become. The Wraith followed behind, sending images for Sheppard to see of ghostly shapes shifting through the trees; stalking him purposefully but enjoying the hunt too much to end it quickly._

_Sheppard could feel the Wraith gaining ground, feel its foul breath wafting down the back of his neck. Stepping up the pace John tripped on a hidden tree root and crashed painfully to the ground, the loud crack and intense pain telling him he'd broken something crucial inside. Moaning in agony Sheppard looked up just in time to see the Wraith almost glide into position above him. The feeding hand slammed onto his chest, familiar and made all the worse because of it. Sheppard screamed at the unbearable pain, almost ready to beg for an end –"_

x

Sheppard came to wakefulness, vaguely aware that his own voice yelling had woken him from the dream. "Damn it!" he growled aloud, troubled by a second unusually vivid dream in the same night. Glancing at the clock he groaned - it was only 4:23am. Still, he didn't want to go back to sleep, didn't want to risk a third nightmare. Dragging himself from the bed, Sheppard changed into his running clothes before heading out into the deserted corridors of Atlantis.


	3. Anything different this morning?

**Chapter 3: Anything different this morning?**

"Are you with us Colonel?" Doctor Weir asked, bringing John's awareness back to the conference room.

"Sorry?" Sheppard glanced around the room, wondering how long he'd been day dreaming. The look on Teyla's face and the fact that Rodney was shaking his head subtly made him realise Elizabeth had probably tried to get his attention more than once.

"I was just wondering if you were intending to join us this morning," Doctor Weir looked at him pointedly, making it clear she was well aware his mind had been elsewhere since the moment he'd sat down.

"Sorry," Sheppard sat up straighter, mentally shaking himself in an effort to clear his befuddled brain. "I was ah ... up early this morning."

"Well perhaps you could make sure you get more sleep next time," Doctor Weir suggested helpfully before returning to the topic of the meeting.

Sheppard still felt disconnected from the conversation, from himself. It wasn't unusual for him to miss sleep – hell he'd gone days without sleep in the past and managed to function better than he was this morning. No, tiredness alone didn't explain his distraction ... the absence of his awareness of Atlantis was just as much to blame. His attention was continually being captured in listening for the city, something he was aware of only when he came back to himself moments later to realise what he'd been doing. Sharpening his focus Sheppard made a conscious effort to pay attention for the rest of the meeting.

Rodney hung back as Doctor Weir dismissed them and the others all left the room.

"Anything different this morning?" Rodney asked cryptically.

"I ah ... haven't checked," Sheppard prevaricated, knowing the continuing absence of the usual hum meant the answer was probably no. Still he sent out an internal request to talk directed at that place within his mind he'd always associated with Atlantis, paused for a few seconds and then shook his head mutely.

"Well the diagnostic came back clean," Rodney reported. "Are you willing to admit there's a problem now?"

"No I'm not Rodney," Sheppard said firmly, getting up and walking quickly from the room.

"But ... you can't just -," Rodney stammered as he almost ran to keep up.

"I _can_," Sheppard insisted, stopping suddenly and turning to face Rodney. He glanced quickly around to make sure no one was listening. "Look," he offered almost hopefully, "maybe I was never meant to have a permanent connection to the city. Maybe the effects of that energy beam wear off over time."

"Did Atlantis ever give you any indication that would happen?" Rodney shook his head in disbelief. "And don't say maybe because I know that's not true. I get that you're not keen on the whole 'my special friend is a city' thing _but_ I think it would be a mistake to ignore the signs of a real problem so you can deny there's anything different about you compared to the rest of us!"

"What do you want from me Rodney?" Sheppard demanded impatiently. "I don't know how the talking thing got switched on ... in fact you have no proof other than my own word that I was ever talking to anyone but myself."

"I saw you in action," Rodney said simply. "That was proof enough."

"All I can do is keep trying to re-establish contact," Sheppard offered that compromise. "Beyond that I'm at a loss just like you."

"And what about that system I wanted to find out about?" Rodney resorted to petty complaints. "We won't be able to do anything with that now."

"I'll come back this afternoon and try to get something out of it for you," Sheppard promised, glad Rodney had finally given up on pushing his connection with Atlantis for now.

x

Instead of heading back to his office Sheppard found himself detouring to his quarters. He felt tired enough that a short nap sounded very appealing. Maybe if he just got a little sleep he wouldn't feel so disconnected from everything, nor so distracted. Stretching out on his bed Sheppard closed his eyes and dropped into a deep sleep.

"_Sheppard," a voice that seemed to be both Wraith and somehow human as well dragged him up from the dark well he'd been lost in. John opened his eyes, not surprised to find himself in that same forest, running through the trees with the sense that something sinister was after him._

"_Colonel?" the voice came again. Sheppard picked up the pace, sprinting away from the source, looking behind him to see if his pursuer was visible._

_Slam! Sheppard's body impacted with something at high speed, throwing him back through the air to land hard on the ground. Winded, Sheppard struggled for breath as he raised himself up to see what he'd hit._

_The Wraith. While Sheppard was still recovering the Wraith leapt up off the ground where he'd fallen, appearing above John in seconds._

"_SHEPPARD!" It was the Wraith and yet not, the contradiction distracting John from his immediate danger. He turned his head to look back into the forest, searching for an explanation. The Wraith put a hand to Sheppard's shoulder, pinning him to the ground. John looked back up to see its feeding hand poised to strike._

"_NO!" Sheppard yelled, panting harshly, trapped in the nightmare world. "Get off me!" Struggling he managed to get a hand free, clamping it fiercely around the Wraith's throat and squeezing as hard as he could. Sheppard was accustomed to holding a P90 steady for hours on end and it pleased him that he could hold on pretty damn hard._

_The Wraith's eyes bulged in its head as it tried to breathe. "Sheppard," it choked out, pleading for new air to fill its starving lungs. John held on grimly as the Wraith grabbed his wrist and tried to pull his hand away. "Jo ... hn," the Wraith gargled torturously. Sheppard flinched at a sudden pain in the hand he wasn't using to squeeze the life from the Wraith. He blinked ..._

... and found himself back in his own quarters with Rodney McKay looming over his bed.

"Ouch!" he snapped to waking instantly, glaring at Rodney angrily. "You bit me!"

"Jo ...hn," Rodney gasped out faintly, still constrained by Sheppard's hand around his throat.

"Crap!" Sheppard let go abruptly, watching sickly as Rodney slumped back to sit on the floor, gulping in huge lungfuls of air. "I _told_ you not to sneak up on me when I'm sleeping!"

"I called you _three_ times!" Rodney protested in a still breathless voice. "You were dreaming ... having a nightmare by the looks of it."

"It wasn't a nightmare!" Sheppard denied angrily. "And you mustn't have called out very loudly if you couldn't wake me up."

"Do you have any idea what time it is?" Rodney asked irritably, getting slowly to his feet and putting a shaky hand to his throat. "You were supposed to come down to the lab hours ago but instead you've been in here sleeping all afternoon."

"You keeping tabs on me now?" Sheppard felt the unreasonable anger bubbling away inside ... he reached for the iron control he usually placed on himself but today he just couldn't find it. He was sick and tired of always being on call – no matter what time of the day or night, sick of people who only ever wanted something from him.

"No," Rodney denied hotly. "It's not like you to break a promise."

"I don't remember promising to be at your beck and call McKay," Sheppard snarled, jumping from the bed and taking a few intimidating steps in Rodney's direction. "In fact I don't recall signing up to be at anyone's beck and call and yet that seems to be what I've got ... twenty four hours a day every bloody day of the week."

"Huh?" Rodney backed away in confusion. "What the hell are you talking about? What's wrong with you?"

"NOTHING!" Sheppard yelled, making Rodney jump fearfully. "Why can't you people just leave me the hell alone for five frigging minutes?!"

"Fine," Rodney's voice fairly dripped with confusion and hurt. "I'll leave you alone ... Colonel. But you should think about what you just said because that's not you."

"Get out," Sheppard's tone was quiet and deadly. He turned away, unwilling to even watch Rodney leaving.

"I'm going," Rodney said quietly. "Oh, and thanks for your concern by the way," he added bitterly. "You almost succeeded in choking me ... and even though you don't appear to care – I'm fine." With that Rodney spun and almost ran from the room.

"RODNEY!" Sheppard ran to the doorway calling for Rodney to stop but it was too late. John couldn't believe what he'd done. He'd almost strangled his best friend and then, instead of saying sorry, instead of insisting Rodney get checked out by Beckett, he'd proceeded to make it worse by yelling at him and practically blaming him for the whole thing.

"_DAMN IT!_" he yelled, punching a fist into the nearest available surface with all his strength. The control panel next to the door was just as unforgiving of him as he was of himself – sharp pain lanced from his fist down his arm at the forceful contact. Looking at his hand in sick detachment he felt a sinking feeling inside when he realised he'd smashed the panel cover, embedding a large jagged piece of hard plastic through the gap between two fingers straight into his palm. His whole hand throbbed which meant at best he'd probably fractured something and blood was flowing freely down his arm and onto the floor. How the hell was he going to explain _that_ to Doctor Beckett?


	4. Four hours, 1 xray, 5 stitches, and

**Chapter 4: Four hours, 1 x-ray, 5 stitches, and two pain killers later**

"What have you done to yourself?" Carson demanded as Sheppard strode into the infirmary a few minutes later, hand wrapped in a towel that was already soaked with blood.

"Why do you always assume I actively contribute whenever I turn up here?" Sheppard complained weakly, letting Beckett assist him up onto an examination bed.

"I've already spoken to Rodney Colonel," Carson cut him off before he could add anything. "Although he didn't warn me about this," Beckett gestured to John's latest injury. "So you can forget about whatever story you've concocted to explain."

"He didn't waste any time," Sheppard muttered grimly, watching as Carson unwrapped the towel to reveal his very swollen and probably broken right hand.

"He's worried about you," Beckett looked at John sternly. "He wouldn't give me all the details but he said you were not yourself ... very badly not yourself."

"He didn't tell you what happened?" Sheppard looked up in surprise.

"No," Beckett confirmed as he administered to John's hand. "Do _you_ want to tell me what happened?"

"Not really," Sheppard looked down glumly.

"Well at the very least I'll need an explanation for what prompted this," he gestured to Sheppard's ruined hand. "The truth lad – I've been around long enough to recognise when a patient's put their fist through something."

"I don't know Carson," John's gaze was troubled as he frowned at the memory of the past hour. "It's like I was in some kind of daze ... I just didn't have the control I usually have. The really bizarre thing is that Rodney didn't even do anything to warrant that level of anger – he's done much worse in the past and I've been able to shrug it off."

"Have you noticed anything else unusual," Doctor Beckett asked casually.

"Ah ... not really," Sheppard replied just as casually.

"So vivid nightmares are usual then are they?" Beckett pinned Sheppard with a stern look.

"McKay!" Sheppard growled irritably. "He didn't tell you I almost strangled him but he _did_ tell you he woke me from a nightmare?"

"You almost strangled Rodney?" Carson zeroed in on that one worrying detail. "Whatever possessed you to –"

"I didn't know I was doing it!" Sheppard broke in to explain. "I was asleep and Rodney must have gotten too close ... my first moment of awareness was waking up with one hand around his throat."

"Ah," Carson nodded in understanding. The Colonel wouldn't be the only military person in Atlantis with the type of training that made a man react to danger before he'd even woken up.

"Look – I've warned him in the past not to sneak up on me like that," Sheppard continued, "but that's no excuse. I should have known he wasn't a danger."

"I'm sure that Rodney will forgive you once he's had a chance to think about it," Beckett said in reassurance. "You can hardly be held accountable for something you didn't know you were doing."

"It's not that simple Doc," Sheppard admitted reluctantly. "I ... ah ... I didn't apologise. In fact I was pretty cruel – and I ah ... I yelled at him."

"Don't worry lad - we'll sort you out here and then you can go and talk to Rodney," Beckett put a comforting hand on Sheppard's shoulder. "First up we need to x-ray your hand."

"Thanks Doc," Sheppard said gratefully.

"Don't thank me just yet Colonel," Doctor Beckett replied. "You know I'll have to report this to Doctor Weir ... she'll want you to talk to Doctor Heightmeyer."

"I knew you were gonna say that," Sheppard grumbled, not sure what was worse - having to sit around talking about his feelings or getting reamed out by Elizabeth.

x

Four hours, 1 x-ray, 5 stitches, and two pain killers later Sheppard was released from the infirmary, right arm plastered from knuckles to mid forearm and supported by a sling. It was late evening and he'd decided the best thing to do would be to talk to Rodney straight away. Even though it was late he knew the lab was probably the most likely place to find him.

"You still need help with that system?" Sheppard held out the olive branch hesitantly, fully expecting Rodney to throw it back in his face.

"Are you offering?" Rodney's voice sounded normal, although he'd yet to turn from his laptop to look at John.

"Yeah," Sheppard agreed, taking a few steps closer.

"I need to finish running this program," Rodney said, hitting a few keys before turning to face Sheppard. He frowned when he noticed the cast and sling. "What did you do now?"

"Came off second best in a disagreement with my door controls," Sheppard quipped with a careless smirk. "Which reminds me – can you send someone down to fix them?"

"Am I the only one worried about you?" Rodney looked at Sheppard intently. "Can you not see that you haven't been yourself lately? And I don't just mean this," Rodney gestured to his own neck and Sheppard noticed for the first time the darkening bruises circling Rodney's throat.

"I'm fine Rodney," Sheppard insisted, "and ah ... I'm really sorry about that," Sheppard waved a hand towards those bruises.

"Not your fault," Rodney said simply. "It's not like you haven't warned me a hundred times not to approach you when you're sleeping."

"I should have known it was you," Sheppard disagreed.

"Under normal circumstances I'd agree with you," Rodney replied, watching John's expression intently. "But this was hardly normal – you were deeply immersed in what looked like a particularly vivid nightmare. Can you remember what it was about?"

"Kolya's pet Wraith," Sheppard said simply. "Look, I'm ... ah ... I'm sorry I yelled at you. I don't even know why I did that."

"Is that how you really feel?" Rodney asked quietly. "That we ... that _I_ expect you to drop everything whenever I call?"

"No!" Sheppard denied. "I had a crappy night's sleep, I was tired and then there were the nightmares. I just needed a break."

"Nightmares?" Rodney leapt on that one. "You've had others?"

"Just a couple last night," Sheppard admitted reluctantly. "It's not that unusual Rodney ... getting the life sucked out of me by a Wraith has gotta have some kind of lasting effect."

"I suppose," Rodney agreed thoughtfully. "But why now? That was over a month ago."

"I don't know," Sheppard replied, "but you'll be glad to know Beckett's also concerned – he wants me to go see Heightmeyer."

"Good," Rodney said unsympathetically. The beeping from his laptop drew Rodney's attention away – after tapping a few more keys he nodded to himself before getting up from his chair. "Shall we try that system again?"

"Sure," Sheppard agreed. He watched Rodney call up the isolated system for a few moments before speaking again. "You should get Carson to check out your throat ... make sure I didn't do any lasting damage."

"Carson already came down to see me," Rodney said lightly. "No permanent damage done. Now, are you ready to try this?"

Sheppard followed Rodney's prompting, mentally leaning on the system controls to try and find out what the system did. As before, those controls were completely unresponsive. This time there was nothing – no pulse of energy, no indication the system was even receiving power.

"Mmm," Rodney said thoughtfully, looking down at the console with a puzzled expression.

"What?" Sheppard asked curiously.

"Oh, nothing," Rodney replied slowly. "I just ... I wondered whether maybe this ... whatever this is was responsible for your nightmares."

"That seems unlikely McKay," Sheppard said in amusement. "It didn't work last time and it's not working now."

"You're right," Rodney agreed. "It was just a thought ... still, I'd really like to know what this system is for."

"Should I try turning it on?" Sheppard asked. "Maybe that's the only way we're gonna find out."

"It's probably not dangerous but we've been burned before with the Ancients," Rodney prevaricated. "You know I'd like to just say yeah, turn it on, but Elizabeth would have my head if it turned out to be something threatening. I don't think she's completely forgiven me yet for draining the ZedPM."

"We wouldn't want to make that worse," Sheppard agreed. "Plus I'm already in trouble because of this," he held up his plastered hand.

"Let's call it quits for now," Rodney suggested, turning back to his laptop. "I'll let you know when Elizabeth approves us taking it further."

"Sure," Sheppard stood in the middle of the lab, waiting for Rodney to notice he hadn't left. When Rodney glanced up with a raised eyebrow Sheppard looked at him seriously. "Are we okay?"

"If by okay you mean have I forgiven you for almost killing me," Rodney said matter-of-factly, "then yes, we're okay."

"Thanks Rodney," Sheppard smiled in relief, taking his leave before Rodney could think of something else he wanted help with.

x

"You had to go and injure yourself again?" Ronon complained the next day at breakfast.

"I didn't do it deliberately," Sheppard shifted uncomfortably at the scrutiny he was getting from the rest of his team.

"You put your fist through your door controls," Rodney took delight in pointing out. "Sounds pretty deliberate to me."

"Don't you have some underling to go and terrorise?" Sheppard asked sarcastically.

"Not right now," Rodney denied airily. "I can hang out here all day."

"Rodney," Teyla admonished. "How long will it take for your hand to heal?" she asked Sheppard.

"Two broken metacarpals equals about six weeks," he admitted reluctantly.

"And I suppose we're off the mission roster for all of that?" Ronon grumbled with a scowl.

"You can volunteer your services to one of the other teams if you like," Sheppard said in annoyance. "And thanks for the concern buddy ... I'm overwhelmed with sympathy here."

"A warrior who can't control his anger doesn't deserve sympathy," Ronon said sternly.

"_Ronon_," Teyla again had to put that scolding edge into her voice. "We are _all_ disappointed the Colonel is injured but that is no excuse to pick at each other."

"Fine," Ronon shoved back from the table, grabbing his tray and striding away without another word.

"He means well,' Teyla excused. "Ronon does not do well with inactivity or confinement."

"Whatever," Sheppard stood up as well, looking at the remaining members of his team. "What I said to Ronon goes for both of you as well – don't let this stop you from going off world. I'm sure Doctor Weir would welcome your help."

"Are you all right John?" Teyla looked at him with concern.

"Sure," Sheppard agreed. "Why wouldn't I be?" Before she could answer Sheppard glanced at his watch as the signal for leaving. "I gotta go ... I'll catch up with you later."

**Authors Note:**

The metacarpals are the bones in your hand between knuckles and wrist ... I guessed the healing time based on a blogspot I found called signmycast that had estimates for wrists (3-8 weeks) and lower arms (6 weeks), so apologies if it's not accurate.


	5. What makes you happy Colonel?

**Chapter 5: What makes you happy Colonel?**

The next few days passed without any new incidents. Sheppard's connection to the city was still strangely absent but John was relieved that Rodney appeared to have given up trying to work out the reason for that. When you couldn't explain in a scientific way why something was there in the first place it didn't leave much hope for explaining why it was suddenly gone.

Sheppard found himself adjusting to the absence, helped in part by the fact that he spent most of his days catching up on the administrative work he usually never had time for. Time passed in a tired distracted blur brought on by nights filled with nightmare Wraith stalking him through the forest of his dreams. He'd taken to avoiding the rest of his team ... Teyla and Ronon were easy because Doctor Weir _had_ utilised them on other off world teams. Rodney was a bit more difficult, persistent in his belief that something was wrong with John despite all his assurances and protests to the contrary.

After cancelling twice at the last minute Sheppard finally had no choice but to turn up for his appointment with Doctor Heightmeyer almost a week after the incident that had prompted the directive from Elizabeth. Normally Rodney would have been happy to listen to Sheppard's complaints about the futility of the whole exercise but not this time - the only thing that seemed to be holding him back from dragging Sheppard back to Doctor Beckett was the knowledge John was getting professional help from _someone_.

"Why do you think you're here today Colonel?" Kate Heightmeyer used that gentle counsellor's voice that always gave him the creeps.

"Because Doctor Weir asked me to speak with you and I couldn't get out of it," Sheppard went for the truthful but unhelpful answer.

"And why do you think she did that?" Kate persisted.

"Because I tried to rearrange my door controls with my fist," Sheppard said glibly. "She and the Doc are worried that's not exactly normal – even for me."

"And what do you think?" Kate's face was expressionless despite John's obvious lack of real cooperation.

"Are you gonna be asking me questions like that for the whole session?" Sheppard looked at Kate with a bland expression. "Because it doesn't make this feel much like an actual ... conversation."

"Please just answer the question Colonel," Kate urged. "It's important in these kinds of sessions for you to guide the process."

"I'll be honest," Sheppard leant back casually in his chair, trying to convince Kate that he was quite comfortable being there. "The only place I'll be guiding this conversation is out the door."

"If you don't cooperate this time Doctor Weir will only insist on a follow up session later," Kate pointed out, not taking offense to a remark that was probably similar to many she faced every day.

"Okay," Sheppard gave in abruptly, his whole demeanour changing to purposeful in the blink of an eye. "No it's not normal – I usually have much better control of my anger than to show it, let alone display it in such an aggressive manner."

"I overheard a couple of Doctor McKay's staff talking about an argument you had with him in the lab the day before the incident," Kate admitted. "That combined with the fact that you felt threatened by Rodney enough to attempt to strangle him doesn't paint a good picture."

"You _have_ been keeping tabs on me haven't you?" Sheppard commented bitterly, "Well your interpretation is somewhat flawed. One – I didn't _argue_ with McKay. It was just a ... lively conversation. And two – I didn't feel threatened by him. I reacted to a foreign presence during my sleep just as I've been trained to do. I didn't even know it was him until _after_ I woke up."

"I understand that Colonel," Kate nodded, "but Doctor Beckett also mentioned some vivid nightmares you've been having lately."

"Isn't it normal having dreams after difficult things have happened to you?" Sheppard turned the question back to the questioner.

"It is," Kate agreed. "And in and of themselves they're not necessarily a problem. But nightmares combined with other things could point to issues that need to be addressed."

"Like what?" Sheppard frowned slightly, feeling a chill dread inside.

"A range of things Colonel," Kate said evasively. "Let's talk about your general wellbeing," she changed the subject abruptly. "Have you made any changes in your routine recently?"

"Um ...," Sheppard thought quickly, trying to decide what that question was supposed to be getting at. "I gave up my morning run with Ronon – but only because of the cast."

"Do you normally take a break from that when you're injured?" Kate's tone was mildly interested.

"Depends on the injury," Sheppard admitted. "I guess I could run with the cast but there's not much point – with this thing weighing me down I've got no hope of beating Ronon."

"Is that what your runs are about – winning?" Kate looked at John curiously.

"Not on the surface," Sheppard grinned, "but deep down - yeah, that's exactly what they're about."

"Are you a planner Colonel?" Kate asked lightly, changing the subject again. When Sheppard raised a puzzled eyebrow at her she rephrased the question. "Do you have clear ideas on what direction you'd like your career – your personal life – to take in the future?"

"I have a dangerous job in a place where we're the primary food source for a race that far outnumbers us," Sheppard said grimly. "So no, planning for the future isn't at the top of my list."

"Have you always been that way?" Sheppard looked at Kate almost suspiciously as she waited for him to think about that one for a moment.

"I don't know," Sheppard finally admitted. "I guess I was more interested in imagining my future at one stage – wouldn't have got married otherwise. But the more time we spend here, the more people we lose to the Wraith ... I don't know," John trailed off uncomfortably.

"What makes you happy Colonel?" Kate moved on to the next topic with barely a pause.

Sheppard took a moment, trying to work out where Heightmeyer was going with her seemingly random mix of questions. "A turkey sandwich at the end of a long shift," he quipped lightly, earning a slight smile from Kate.

"When was the last time you felt genuinely excited about something?" Kate persisted, turning the question around and sending it straight back to him.

"Ah ...," Sheppard ran a hand over the back of his neck as he tried to think of something. "When the SGC re-established contact with us I guess," he said hesitantly. Surely there was something else more recent that he'd gotten excited about but for the life of him he couldn't bring anything else to mind.

"That was a long time ago," Kate pointed out. "Nothing more recent?"

"Probably," Sheppard agreed. "I just can't think of anything right now. Once I walk out that door I'm sure a million examples will occur to me."

"I'm sure they will," Kate smiled easily. "Getting back to the anger you mentioned before, can you tell me a bit more about what you were thinking at the time?"

Sheppard cooperated as best he could, fielding question after question about his actions and his motivations. He could feel himself getting more and more impatient before finally Doctor Heightmeyer called the session to a close. Sheppard wasted no time in jumping up and taking his leave – purposefully giving no further thought to the outcome.

x

"Sit down Colonel," Beckett gestured to the chair across from his own.

"What's the story Doc?" Sheppard asked, curious about why Carson would have called him into his office for a private chat.

"I spoke with Doctor Heightmeyer after your session with her yesterday," Carson began. "She feels, and I agree, that there are a few issues emerging for you that we need to pay attention to."

"Not the thing with the nightmares again," Sheppard complained. "Surely I'm allowed a little time to deal with surviving a Wraith feeding attack!"

"If it were just that I'd agree with you Colonel," Beckett replied. "But your memories of that event are affecting your work as well – Elizabeth isn't the only one to tell me how distracted you've been lately. Plus Dr Heightmeyer felt you were showing signs of disinterest in your usual activities, along with no desire to plan even for your immediate future."

"So?" Sheppard asked in confusion. "Just get to the point Carson!"

"You're well on the way to a case of Post Traumatic Stress Disorder son," Beckett said grimly.

**Authors Note:**

Things are only getting worse for Shep ... don't hurt me though ... there's progress ahead ... somewhere ...

Thanks to Dybdahl (of course I believed you!) for letting me know my Ronon spelling was wrong ... lucky it was just the last chapter so far and the rest of the story has now been corrected (plus all my other stories!!).


	6. I can see where this is going now

**Chapter 6: I can see where this is going now.**

"What?" Sheppard gaped at Beckett is shock. "You can't be serious Carson!"

"Oh I am," Beckett said sternly, 'and you better get serious too because this isn't something to joke about. You're not there yet but if we don't do something to alleviate the stress you're under I'll have no choice but to treat you as a PTSD patient."

"I don't have Post Traumatic Stress Disorder!" Sheppard denied heatedly. When Beckett had told him he needed to have a chat this was so not what he'd expected.

"Not yet," Carson reiterated. "But Doctor Heightmeyer and I both agree that unless we can address some of your symptoms now you _will, _and in the very near future."

"If a couple of nightmares and the urge to slam your fist through the wall are symptoms then you better start treating half the people on this base," Sheppard said snidely.

"It's more than that John and you know it," Carson countered. "When was the last time you had a full night's sleep?"

"I've never been a great sleeper Carson," Sheppard avoided giving an actual answer. "That hasn't changed."

"Almost two weeks Colonel," Carson provided the answer himself. "And the nightmares?" he persisted. "They've been getting worse haven't they?"

"I can see where this is going now," Sheppard got up abruptly, glaring down at Beckett. "It's not about whether I've got PTSD – it's about whether you _think_ I've got it. Nothing I say is gonna change your opinion is it?"

"There are standard sets of questions used to diagnose this sort of thing," Carson didn't deny Sheppard's accusation. "If you took that questionnaire – _honestly_ – you'd be classed as borderline. Why risk making that worse when with a bit of effort you can turn it around?"

"_Because I don't have PTSD!_" Sheppard raised his voice angrily. "This is all a bunch of horseshit." Not waiting for Doctor Beckett to say anything further, Sheppard turned and stormed out of the office.

x

"They think I've got PTSD Rodney," Sheppard paced in agitation around Rodney's lab. His head felt full ... disturbing thoughts and worries buzzing around and adding to the strange mix of disconnection and panic he was feeling.

"Would that be a bad thing if the treatment means you stop having nightmares?" Rodney asked hesitantly.

"You think they let PTSD patients run military bases?" Sheppard's tone was sarcastic but it annoyed him that he couldn't keep all of the worry he was feeling out of his voice.

"You haven't had a break in more than two years," Rodney pointed out. "Take some time, get fixed up, come back – it's a no brainer."

"I don't want a break," Sheppard said heatedly. "What would I do with myself all day? I'd have too much time to think and that can only end in disaster. Besides, you haven't had a break either!"

"But I'm not waking up in a cold sweat screaming the place down two or three times a night either," Rodney said grimly. "In a way this even makes sense."

"How could this possibly make _sense_?" Sheppard demanded.

"Well the timing _is_ a little coincidental," Rodney pointed out. "You lose your connection to Atlantis just when the symptoms start presenting themselves. I was thinking that system did something _to_ you but maybe it's much simpler than that. Maybe Atlantis _can't_ communicate with you _because_ of your mental state. You get fixed up and you'll hear her again."

"For the last time McKay, there's _nothing_ wrong with me," Sheppard growled, glaring at Rodney in frustration.

"You need help John," Rodney said quietly. "Please don't be stubborn about this."

"_I need help?!_" Sheppard's volume rose sharply. "That's just great coming from you McKay." Sheppard clenched his hands at his sides as he started pacing, breath going in and out much too rapidly.

"Calm down before you blow a fuse," Rodney advised, appearing remarkably calm in the face of an angry and agitated Sheppard.

"I am _sick_ of this crap," John turned away in frustration. "Sick of risking my life for a bunch of ungrateful rats who turn against me at the first sign of trouble. Sick of giving my all and getting _nothing_ in return. You're right – maybe I should have a break. No, no – better than that – maybe I should just leave," Sheppard didn't know what was driving him, didn't know where all this was coming from but he was powerless to stop it. "I never wanted this job in the first place and it's not like the powers that be wanted me either. You'd all be happy then wouldn't you – no more moody face to ruin your little happy place."

"Sheppard," Rodney broke in, concern written all over his face. "Listen to yourself ... what you're saying right now should be your biggest clue that you've got issues to deal with. Instead of complaining about it why don't you just give in and fix it. Then we can go back to business as usual."

"If I give in to this Rodney," Sheppard punched out the words between rapid breaths, "there will _never_ be business as usual again." He hardly heard Rodney's reply, the pounding in his head combined with the lack of oxygen in his lungs (despite the number of breaths he was gulping in) was making him very light headed. On top of that was the sudden inexplicable wave of tiredness that swept over him, his energy drained by some external force. He almost heard the pop inside his skull when the pressure became too much – clutching his head convulsively he toppled over sideways, surrendering to the calming darkness.

x

"_Come to me_," a single voice called. "_I need you ... hear my words._"

Sheppard awoke in the darkness of the infirmary, the faint echo of words fading before he could capture them to consciousness. He tried to reach up and run a hand through his hair ... frowning when he realised he couldn't move his arms, and not just because he was immobilised by the cast and sling.

"Carson!" he yelled, waiting impatiently for the Doc to appear. "_Carson_!" A minute or so later Beckett appeared at Sheppard's bedside. "Restraints? You've got me in _restraints?_!"

"You were very agitated Colonel," Doctor Beckett excused. "We were concerned you might injure yourself flailing around as you were ... if you promise to keep a lid on your hostility I'll remove the restraints."

"I can do that," Sheppard agreed easily, watching silently as Carson unbuckled each restraint in turn. "What happened?"

"You don't remember?" Beckett looked up in surprise.

"Ah ... not sure what I'm supposed to be remembering," Sheppard waited for Beckett to fill him in.

"What's the last thing you _can_ recall?" Carson asked in concern.

"Storming out of here after you told me about the possible PTSD," Sheppard replied immediately.

"Apparently you went from here straight to Rodney's lab," Beckett offered. "Rodney said you were very agitated and that eventually something seemed to snap in your head and you dropped to the floor unconscious. I've performed a number of scans and other tests and luckily couldn't find any permanent damage."

"I don't remember any of that," Sheppard said with a worried frown. "Is that another PTSD thing?"

"Maybe," Beckett admitted. "You didn't let me finish our discussion this afternoon – I was going to offer you a range of possible treatment options. Cognitive therapy, exposure therapy, eye movement desensitization and reprocessing. There are also medications - selective serotonin reuptake inhibitors – that are very effective. Given the severity of your latest symptoms I believe we should start you on the medications first – relieve the immediate stresses so we can deal with your longer term recovery."

"This feels all wrong Carson," Sheppard put a hand to his forehead, cringing internally when he realised he couldn't control a faint tremor. "Are you sure about this?"

"As sure as we can be," Doctor Beckett said sadly. "It'll be all right lad ... treatments for PTSD are usually very successful. We'll have you back to your old self in no time."

Nodding wordlessly, Sheppard slumped back on the bed, closing his eyes to block out the sight of Beckett administering his medications through the IV drip attached to his left hand. He'd prided himself on his strong mental capacity ... proved it more than once against Wraith Hive Queens. It was galling to admit that he'd been broken – that something as simple as a Wraith feeding had brought him down. The treatments might help with his mental processes - switch off the nightmares, the worries and the fears - but he was scared they'd never repair his image of himself. If he didn't have that, did he have anything at all?


	7. It was an urge I just couldn’t ignore

**Chapter 7:** **It was an urge I just couldn't ignore**

"_Come to me ... child of the ancestors_," the words from a single voice echoed in Sheppard's head, discordant but somehow alluring. Sheppard frowned in confusion, hearing the call and feeling drawn to find it.

Opening eyes that were blank as though still open to the dream world, Sheppard sat up. Barely flinching he pulled the IV needle from his hand, rose slowly from the infirmary bed and padded softly from the room on bare feet.

"_Yes_," the voice exalted. "_Hear me ... find me_."

Barely aware of the journey Sheppard walked silently until he was standing in front of one of the lesser used transporters. He stepped purposefully inside, tapping a spot on the map of the city that seemed more interesting than anywhere else. Bright light flashed and the doors slid open silently.

Sheppard stepped out into the corridor, pausing to cock his head to the side as though scenting the very air. As in the transporter, one direction called to him more than the others and he set off confidently.

"_You draw near_," the voice confirmed he was on the right track.

This part of the city was silent and dark, minimal lighting switching on to guide his path before switching off again behind him. Sheppard hardly noticed his surroundings, focussing everything on arriving at the part of the city that called to him the most.

Some minutes later his path led him to a door.

"_You arrive!_" the voice cried joyfully.

Sheppard swiped a hand over the door control, stepping into the darkened room. The lights came on instantly, illuminating a single figure standing in the centre of the room. She was the most beautiful woman Sheppard had ever seen – translucent skin a perfection of tone and texture, lustrous black hair falling in waves down a slender back, vibrant green eyes shining with wisdom and something else Sheppard struggled to define. She was dressed in an elegant white dress similar to the ones Sheppard had seen in the Ancient archives and on the figure in the hologram room.

"Who are you?" he asked hesitantly.

"I am Atlantis," the woman replied regally.

"What? H ... how?" Sheppard stuttered, unable to comprehend what his eyes were telling him was plainly true.

"Long have I desired to show myself to you in this form," Atlantis intoned. "It has taken some time for you to be able to comprehend my existence on a level necessary for you to be able to see me."

"Are you really there?" Sheppard frowned as he tried to understand. "Will the others be able to see you?" Before the woman could answer those questions Sheppard thought of something else. "Is this why I haven't been able to communicate with you lately – because you've been working on doing this?"

"So many questions," Atlantis said with amusement. "You descendants of the creators are such a curious people ... more so than the original evolution of humans."

"Am I the only one who'll be able to see you?" Sheppard picked the question he most needed an answer to.

"I am afraid so," Atlantis said somewhat sadly. "No others amongst you possess the creator's genes in sufficient purity to allow the level of communication required for me to achieve this state."

"So why draw me here?" Sheppard was starting to wake from the stupor he'd been in since he'd left the infirmary. "Couldn't you have appeared anywhere? I mean isn't this all taking place in my head?"

"I am separate from your mind John Sheppard," Atlantis countered. "Only in this location am I able to draw sufficient power to appear to you."

"Well at least the others don't have to witness me talking to myself," Sheppard muttered half under his breath. "With everything else going on right now the last thing I need is another symptom I'm crazy."

"I can help you fix your current problems," Atlantis offered. "In fact I can help you unlock all the secrets to this city ... and every system within it."

"But that's not what we agreed to," Sheppard frowned in confusion. "You know I don't want us being handed knowledge without having to work for it!"

"I do," Atlantis agreed blandly. "However, there are difficult times ahead. If I am to survive _with_ you then I must bring you up to the level necessary to ensure that. Now that I am able to appear to you in this form it will be much easier for me to impart that which you need to know."

"Yeah, okay maybe," Sheppard replied hesitantly. "But how are you going to fix my problems with Doctor Beckett?" Sheppard couldn't see how anyone could fix those – not without going down the unappealing path Carson had already mapped out for him.

"I can –," Atlantis broke off, turning her head to glance in irritation at the closed door. "They come – you must leave this place immediately."

"Huh?" Sheppard frowned in confusion. "Why?"

"It will be harder for me to resolve your current concerns if they find you in here," Atlantis insisted, spearing Sheppard with the intense look in her eyes. "If you would have my assistance in the future you must allow yourself to be guided by my greater wisdom. Tell no one that you have seen me!"

"Fine," Sheppard grumbled, disturbed by the show of strong emotions that seemed out of character for Atlantis. Shaking his head at the idea that a city could _have_ a 'character' Sheppard strode out the door and back down the hallway.

"Sheppard!" Rodney called out to him as they each rounded a corner and found themselves at opposite ends of a long corridor.

"What are you doing down here McKay?" Sheppard called back casually.

"What I am doing here?" Rodney's mouth hung open in shock. "_What am I doing here?_ You release yourself from the infirmary almost in the middle of the night, walk down here in your scrubs, not even stopping to put on some shoes, and you want to know what _I'm_ doing here?"

"I ah ... had to walk off some excess energy," Sheppard offered, still strolling at an easy pace down the hall towards Rodney. "Had to clear my head ... I had a really bad day so sue me if I forgot to put on my shoes!"

"This is wrong on so many levels I can barely define them," Rodney muttered, glancing behind him nervously. "I suggest you work out a better story to explain all this because Carson's gonna be here in a few seconds and he is majorly pissed at you."

"I can handle the Doc," Sheppard said with a confident tone not matched by his troubled expression. Pasting an easy going look on his face just in time he smiled weakly when Doctor Beckett arrived.

"Lieutenant Colonel Sheppard," Beckett greeted him sternly. "The fact that you're down here instead of being in the infirmary where I left you tells me one of two things. Either you're stupid lad or your PTSD is progressing at a rate that is frankly _very_ concerning."

"Then I guess I'm stupid Doc," Sheppard replied cheekily. "I couldn't sleep – I just needed a few moments completely alone to you know ... decide on how I want to deal with the whole ... stress thing."

"And you couldn't get that back in your quarters or somewhere closer to the infirmary?' Beckett demanded incredulously. "You had to walk all the way down here, worrying us in the process?"

"Sorry Doc," Sheppard muttered apologetically. "I wasn't thinking ... it was an urge I just couldn't ignore. I honestly didn't think you'd mind."

"Okay son," Beckett relaxed a little in the face of Sheppard's genuine remorse. "But in future talk to me first, _before_ you decide to traipse all over the city in your pyjamas."

"Of course," Sheppard agreed readily, throwing a smug look at Rodney as if to say 'see – I told you I could handle him'.

Rodney and Carson escorted Sheppard back to the infirmary, Rodney hanging around until John was once again settled back into bed. Sheppard breathed a sigh of relief when they finally left him alone after he'd sworn he'd remain there for the rest of the night. He turned his thoughts immediately to what had happened in that isolated room.

Atlantis was a real, physical being – to him at least - determined to give him everything they'd been missing since they'd arrived. Explanations and instructions for systems that were still a mystery. The locations for new systems and information they weren't even aware of yet. It was such a complete turnaround on what they'd agreed when he'd first started talking with Atlantis that it left him troubled instead of excited.

He wanted to accept everything at face value but almost three years in the Pegasus Galaxy had taught him that _nothing_ could be taken for granted. Somehow he'd have to find out more while at the same time not providing any further evidence to confirm that he was going off the deep end. And how the hell was he gonna do that?!


	8. My patience is not unlimited

**Chapter 8: My patience is not unlimited**

"When can I get out of here Doc?" Sheppard quizzed Carson the next morning.

"Let me do a few tests, have Doctor Heightmeyer come down and talk to you first," Beckett replied. "If we're both satisfied with your current condition I'll release you to your quarters but only on the condition that you report in here every four hours."

"I'm still capable of doing my job!" Sheppard protested.

"Let's not talk about that at this stage," Beckett's tone allowed for some hope on that score. "You suffered a high stress episode yesterday ... we need to make sure the medication is doing its job before we add any more pressure into the mix."

"Okay," Sheppard agreed reluctantly. "Can I at least go for a jog ... or do something else physical? I'm not used to all this sitting around."

"I'll have Ronon take you through some light exercises in the gym Colonel," Beckett suggested a compromise. "That should be sufficient for now."

The tests and the talk with Heightmeyer were conducted promptly. Sheppard couldn't influence the results from medical tests but he was smart enough to know what Kate was looking for and controlled enough to deliver it ... now he knew what her thoughts were regarding his condition. It was no surprise therefore when three hours later Sheppard was released from the infirmary.

Knowing more than the usual amount of attention would be paid to his movements Sheppard did exactly what everyone expected for the rest of the day and all through the night. He didn't know if it was the medications or his firm resolve to work things out but he managed his first night of undisturbed sleep for almost two weeks, waking up refreshed and feeling better than he had in a long time.

He obviously still had issues though, something brought home by the conversation he overheard as he was arriving at the infirmary for the first promised check-in the next day.

"I know its selfish Carson," Rodney was saying. "It's just ... seeing Sheppard tormented by his own mind ... it threatens everything! I mean – how can I focus on what I do best if Sheppard isn't there to protect me?"

"The Colonel will recover from this Rodney," Beckett said reassuringly. "You just have to give him some time."

"Yeah, and what happens if the next crisis comes along before he's up to it?" Rodney's voice was dejected now.

Deciding he'd heard more than enough Sheppard concentrated on putting a carefree look on his face before clearing his throat noisily as he walked into the infirmary. Rodney greeted Sheppard awkwardly before making an excuse for a hasty exit.

"How are you feeling lad?" Doctor Beckett greeted him with a sincere smile.

"Something you're doing must be working Doc," Sheppard replied, "because things feel like they're finally looking up."

"Let's not get ahead of ourselves Colonel," Beckett cautioned. "It's not unusual for the medications to provide a level of ... euphoria that won't be sustained in the longer term."

"Yeah – okay," Sheppard said reluctantly. "So can I get back to work today?" Sheppard looked at Beckett hopefully.

"I'll clear you to spend a few hours in your office," Beckett offered. "Plus you can go for a jog this afternoon if you still want to ... just a short one mind and no pushing yourself too hard."

"Thanks Doc," Sheppard smiled gratefully, cooperating with the rest of Carson's examination with plans for the day zooming around his head.

Once ensconced in his office Sheppard called up a link to the Ancient database. He wasn't sure quite what to search for ... cursing the fact he couldn't bring Rodney into this, he started typing.

It wasn't much, but after more than three hours of searching fruitlessly, Sheppard finally found something that might be relevant to his current situation. In an obscure part of the system he'd found reference to an avatar. If he understood the term correctly, in the computing world an avatar was a user's representation of themselves often as a three-dimensional model within a virtual reality. The avatar was supposed to represent the embodiment of the user, the personality connecting the user to their identity within a system. In that context in made sense that Atlantis would have an avatar within the Ancient systems. The only problem with that was how Atlantis had made the shift from the virtual world inside the systems to be able to appear to him in physical form.

Deciding he needed some thinking time before going back to search some more, Sheppard went to his quarters to change before heading out for his jog.

John hadn't really planned out an actual route for his run – deep in thought he let his instincts guide him. Ten minutes later he turned a corner and came to the corridor leading to _the_ room.

"You have returned," Atlantis greeted him, standing in the middle of the room as before. Sheppard wondered for a moment if she'd been standing there the whole time or taken corporeal form only seconds before he'd opened the door.

"Yes," he said simply. "I wanted to know more ... about how you can help us."

"It was to be expected," Atlantis replied with a knowing smile. "Would you escort me from this room so that I might show you more?"

"Ah," Sheppard hesitated. "I thought you said you needed the power you can only get in this room to make yourself visible like this."

"That _was_ the case yesterday," Atlantis agreed. "Since your last visit I was able to create a virtual bridge from this room such that I can take my link to the power source wherever it is needed within the city."

"Oh," Sheppard nodded uncertainly. "Um ... okay then. What did you want to show me?"

Rather than speak, Atlantis held out a hand to Sheppard, waiting expectantly. John reached out slowly, fully believing his hand would pass right through the hand of Atlantis.

Warm fingers met his and clasped tightly. Sheppard raised startled eyes to Atlantis, glimpsing the look of satisfaction before it was replaced with an expression of bland interest.

"Where to?" he asked curiously.

"There is a laboratory at the top of the main tower," Atlantis said intently. "From there I will be able to show you how to access everything you ever wanted to know about this city."

"Colonel Sheppard?" John stopped, holding up a hand to Atlantis as he tapped his earpiece to respond to Doctor Beckett.

"Sheppard here."

"Where are you lad?" Carson's tone was mildly curious but when Sheppard glanced at his watch he cursed under his breath. He was overdue to check in at the infirmary.

"Sorry Doc," he said quickly. "I'm on my way now."

"See you in a few minutes," Beckett's voice warned that if he didn't show up within that time there'd be explaining to do.

"We'll have to do this later," Sheppard turned back to Atlantis.

"Are you so weak that you would let your Doctor dictate where you should be and when?" Atlantis challenged him.

"The last thing I need, _we_ need, is for undue attention to be paid to my comings and goings," Sheppard said reasonably. Inside however the alarm bells were starting to take shape.

"If you escort me from this room and take me to the tower laboratory all your other problems will cease to exist," a hint of bribery had crept into both Atlantis's tone and the expression on her face.

"Forgive me if I'm sceptical you can actually live up to that," Sheppard replied. "I'll check in with Carson and be back here inside a few hours."

"My patience is not unlimited John Sheppard," Atlantis intoned dismissively. "Keep me waiting and my offer to reveal all may be scaled back."

"You've waited this long to share what you know," Sheppard pointed out logically. "Surely a few more hours isn't going to make a difference."

"It is not for one such as you to decide what will and will not make a difference to me," Atlantis retorted heatedly.

Sheppard took a step back, face displaying clearly that he was more than a little troubled by the unreasonable reaction. He watched as Atlantis visibly reigned in her strong emotions, watched the bland expression of mild interest settle back over her beautiful features.

"Forgive me," she said lightly. "The effort required to maintain this form is draining ... I am not myself."

"I'll come back as soon as I can," Sheppard promised. "Maybe you should rest ... whereever it is you usually do that," John gestured vaguely towards the console.

"Perhaps you are right," Atlantis agreed. "I will await your return." she turned her back on Sheppard, standing stiffly in the middle of the room much as he'd found her when he arrived.

Frowning worriedly, Sheppard looked at her for a few seconds before turning and jogging from the room.


	9. In the end they will all abandon you

**Chapter 9: In the end they will all abandon you**

Sheppard sprinted to get back to the infirmary within the few minutes he'd promised Doctor Beckett. He took the scolding without comment, agreed to make sure he was on time for the next check-in, even gave in when Carson suggested he should retire to his quarters for a rest before returning to his office.

Lying on his bed, Sheppard gazed sightlessly up at the ceiling as he idly tossed a ball into the air, letting gravity carry it back into his waiting hands.

The more time he spent with the avatar of Atlantis the more confused he felt. It hardly seemed possible that the city, a collection of systems working in perfect synchronisation, would be embodied by someone so ... emotional. And what a range of emotions to display within the space of minutes! Superiority, condescension, smug satisfaction, and impatience – and they were the milder of the emotions he'd seen. More worrying was the attempted bribery, threats, and general contempt for humans.

He didn't know what to make of it ... all he did know was that until he could find out more there was no way he could go along with anything Atlantis asked of him. He needed help ... the kind he could only get from Rodney.

Yawning tiredly, Sheppard rolled over and buried his head in the pillows, wondering why for once something _couldn't_ be as good as it seemed.

x

"_You cannot save him," the Wraith snarled. Sheppard pulled and strained at the ropes that bound him but couldn't move an inch. He watched helplessly as the Wraith ripped open the shirt of Doctor Rodney McKay, grinning at John tauntingly as it prepared to feed. Sheppard looked into the tormented eyes of his friend, regretting the fear and the unwelcome knowledge displayed there. Rodney knew now what it took to break him ... something he'd probably never recover from._

"_John," Rodney pleaded tearfully, bracing himself for what he knew was about to happen. "Do something!"_

"_I'm sorry Rodney," Sheppard croaked, still straining against his restraints. "I've tried but ... I just can't get free."_

"_You call this friendship?" the Wraith sneered. "You humans know nothing of true brotherhood ... willing as you are to give each other up for the chance of salvation."_

"_That's not true," Rodney denied weakly, cringing away as the Wraith leaned in menacingly._

"_Isn't it Doctor McKay?" the Wraith asked knowingly. "And if I were to offer you _your_ freedom in exchange for the life of Colonel Sheppard?"_

_Rodney whimpered in distress, eyes gazing at Sheppard mutely before he turned resolutely away and nodded once._

_The Wraith laughed in delight as it moved to Rodney's side, quickly cutting the ropes that had bound him in place. "Go human weakling," it urged._

"_Sorry," Rodney muttered under his breath, eyes fixed on the ground so he wouldn't have to see the devastated expression in John's eyes._

_Sheppard watched in disbelief as Rodney turned and scrambled through the trees to safety without a backward glance._

"_You see human?" the Wraith taunted, stalking across to its captive. "In the end they will all abandon you."_

_Sheppard flinched as the Wraith slammed its feeding hand down firmly on his chest. As he screamed in agony he wasn't sure what hurt worse – having the life sucked out of him in the physical sense by the Wraith, or mentally by the knowledge that everything he'd believed about his own worth had turned out to be a lie._

x

Sheppard lurched from the bed moaning in distress at the worst nightmare yet. Stumbling to the bathroom he fell to his knees, leaning over weakly to eject the meagre contents of his stomach. When there was nothing else to get rid of and his dry retching had dissipated he curled up on the floor, shivering despite the fact that it wasn't cold.

It took a while to recover, a while for the suspicions to surface. He'd been thinking about letting Rodney in on the secret and then he had a dream where Rodney betrayed him? Could that really just be a coincidence? In the end the answer didn't really matter – if Sheppard was going to work out what was going on he needed help from someone not so intimately connected to the source.

Pulling himself up from the floor John rinsed his mouth and splashed water on his face to wake himself up. It shocked him to see his reflection in the mirror – visible lines of torment on his face, black circles under his eyes despite the full night of sleep he'd had the night before. A good thing from the convincing perspective though – how could Rodney fail to believe the depths of John's issues when they were plainly etched into his face?!

x

"I've got a problem Rodney," Sheppard stalked into the lab a short time later, relieved that Rodney was by himself.

"Apart from the fact that you look like hell?" Rodney replied, glancing up briefly to assess Sheppard's condition before returning his attention to his work.

"I'm serious McKay," Sheppard put some steel into his voice, enough for Rodney to sit up and take notice.

"Okay, what is it?" Rodney folded his arms across his chest and waited for John to speak.

"This will be much easier if you just let me show you," Sheppard raised an eyebrow, waiting for a reaction. Even though the avatar had told him no one else would be able to see her, John was pretty confident there'd be enough detail available on the console in her room to convince even Rodney that she existed.

"Fine," Rodney got up reluctantly. "But this better be good."

"_Oh it is_," Sheppard promised, leading the way from the lab. "This is probably the biggest thing you've found out about since we got here."

"Bigger than Atlantis talking to you?" Rodney retorted in disbelief.

"_Much_ bigger," Sheppard insisted, urging Rodney to hurry.

Rodney remained silent for the rest of the journey as Sheppard led him to the transporter and out into now familiar darkened corridors in the depths of the city. As John got closer to the room he felt a curious lethargy sweeping over him, steadily increasing to the point that he found he couldn't bring himself to open the door once they'd arrived.

"Is this it?" Rodney asked curiously. Sheppard felt his throat close over, the sudden dryness making it hard for him to speak.

"Inside," he croaked. "You might need to go in without me ... look at –," Sheppard broke off suddenly, frozen in place by the shift in his reality.

"Sheppard?" John could just hear Rodney's voice - just feel the hand on his arm shaking him in concern - but he couldn't respond. In front of his eyes he could make out the faint outline of Rodney looking at him in concern but overlaid on top of that was the face of his Wraith torturer, feeding hand outstretched in preparation.

"_Snap out of it!_" Rodney yelled, shaking John's shoulder firmly and bringing himself to the forefront of Sheppard's attention.

"Rod ... ney," Sheppard focussed weakly on his friend as he grated out, "check ... the ... con ... sole." He swayed dizzily, the strength leaving his legs so quickly that he couldn't hold himself upright anymore. He hit the ground awkwardly, putting his broken hand down first and then crumpling over it when it couldn't hold his weight. That pain was enough to stop the Wraith vision from taking hold again. Sheppard groaned weakly, curling into a ball on the floor and cradling his plastered arm.

"_Medical emergency to section F corridor 3_," Rodney called urgently, dropping to the ground beside him. Sheppard kept his eyes fixed to Rodney's face, unable to speak through a throat still constricted. Rodney looked ready to hit something in frustration himself by the time Beckett arrived with a medical team.

"What happened this time?" Carson demanded, moving in quickly to check on Sheppard's condition.

"More of the same," Rodney said reluctantly. "He went into some kind of trance and then collapsed. I think this," he gestured to the signs of pain Sheppard couldn't hide, "is because he fell on his injured arm."

"Hey," Sheppard finally managed to protest weakly, "_he_ is right here!"

"Okay Colonel, let's get you back to the infirmary," Doctor Beckett ordered. Sheppard submitted to being transferred to a gurney without the usual complaints, wordlessly trying to communicate to Rodney the importance of what he'd wanted to show him. "Are you coming?" Carson asked Rodney expectantly.

"He's gonna be all right isn't he?" Rodney was still looking at John in concern. When Beckett responded in the affirmative, Rodney gestured towards the room. "I'll be there soon - I want to check this out first."

Sheppard relaxed onto the gurney, sighing in relief now he knew Rodney was on board.


	10. What does this avatar want?

**Chapter 10: What does this avatar want?**

"Did you check the console?" Those were the first words Sheppard spoke when he awoke in the infirmary later that night to see Rodney sitting beside his bed.

"I did," Rodney agreed. "What did you think I was going to find?"

"It's an avatar," Sheppard said, watching for Rodney's reaction. "She lured me down there ... I don't know how but she's manipulating me so I'll do what she wants."

"She?" Rodney raised an eyebrow expectantly.

"_Atlantis_," Sheppard said insistently. "The avatar is a physical representation of Atlantis ... only she's nothing like I would have expected. She's emotional, angry and impatient, and she clearly wanted _something_ from me."

"You might be on to something," Rodney leant in to speak as privately as possible. "That console gave me access to a whole host of information about the room. Power consumption, imaging records ... there's evidence of a virtual environment existing within the system."

"So she really is real?" Sheppard felt the relief deep down inside. A small part of him had worried that perhaps everything he'd seen, entire conversations with Atlantis, had all been in his head - a part of the whole PTSD thing.

"You doubted it?" Rodney asked, nodding when Sheppard looked at him blandly rather than admit that he had. "Well in this case I don't blame you – whatever this thing is, she's gone to great lengths to cover her tracks. There wasn't any evidence of her appearing outside of that system."

"You don't think it's Atlantis?" Sheppard picked up on that part of Rodney's statement immediately.

"You said it yourself," Rodney replied. "The avatar is nothing like you expected ... you just assumed it was Atlantis because it said so. It's not like you to be so trusting."

"Yeah well Atlantis is the first computer system I've spoken to so intimately – I don't exactly have experience with this!" Sheppard said heatedly. "If it isn't Atlantis how come I'm the only one who can see and talk to her?"

"I don't know," Rodney protested. "I'm just saying don't believe what she tells you just because she said she was Atlantis!"

Calming down slightly Sheppard ran a hand across the back of his neck, looking at Rodney pointedly. "What are we gonna do about this?" Sheppard crossed his mental fingers, hoping that once again Rodney would have a plan to fix things.

"We need more information which means we need to get you out of the infirmary and out from under the suspicion of post traumatic stress disorder," Rodney said firmly. "To do that you have to come clean with everyone about your real connection to Atlantis."

"Rodney," Sheppard winced at the idea. "Everyone already thinks I'm only steps away from being crazy. How is telling them I could talk to the city in my head but now I can do it in person going to make that better?"

"Unless you give them another scenario that explains all your symptoms they're gonna continue to blame everything on the PTSD," Rodney pointed out. "We have to take that out of the equation if we're gonna work out what's really going on. Don't worry - I'll back you up."

"How are we going to stop her from retaliating with more disturbing nightmares?" Sheppard countered. "I'm surprised she's even letting me talk to you like this!"

"I have one idea," Rodney admitted, "but it won't be comfortable – for either of us".

x

"Okay John," Doctor Weir sat at the head of the conference table, surrounded by Doctor Beckett and the rest of team Sheppard, Doctor Zelenka and Major Lorne. "We're all here ... what did you want to tell us?"

"I'm just gonna jump right in," Sheppard said, having already psyched himself up for what he knew would be a difficult few minutes. "This will sound crazy, especially given my recent ... issues. You all know I've always had a deeper connection to the Ancient technology that anyone else with the ATA gene. What you don't know is how deep that connection goes."

Pausing for a moment, Sheppard glanced quickly at the occupants of the room. Elizabeth looked like she knew what to expect and was wondering why John would bother bringing it up. Rodney looked like he was trying to send Sheppard support through the intensity of his gaze. Everyone else just looked confused.

"I can hear the city," Sheppard said quickly, "and I'm not just talking about the hum you know about Elizabeth. I'm talking about actual words ... hell whole conversations."

"You've been _talking_ to Atlantis?" Elizabeth asked with disbelief evident in her voice.

"Since the hydrothermal vent," Sheppard confirmed. "Before that it was just a hum in my head because I was blocking it out. After I got hit with that energy beam I couldn't do that anymore and Atlantis ... spoke to me."

"Why would you keep this from us John?" Teyla asked intently. "My people believe your connection to the city is a gift from the Ancestors. Something you should celebrate, not hide."

"Politics," Elizabeth said simply. "Our positions here are controlled by the military back on Earth, and more importantly by the International Oversight Advisory. If they learn how far John's connection goes they'll want to see if there's any way they can exploit it."

"Is there any proof beyond your word?" Doctor Beckett asked reluctantly.

"No," Sheppard replied starkly. "Are you suggesting my word is no longer good enough?"

"Of course not son," Carson denied. "But the changes you're talking about happened _after_ your last encounter with Kolya. It was a horrible, traumatic thing that happened to you – for once you can't deny that because we all witnessed some of it. Everything you're describing could equally be explained by Post Traumatic Stress Disorder."

"It's real," Rodney spoke up for the first time. "I saw Sheppard in action myself."

"Wait," Doctor Weir held up a hand, glaring at Sheppard in annoyance. "You told _Rodney_ but you didn't inform me?"

"Um ...," Sheppard looked across at Rodney before turning back to Elizabeth. "Blocking communication got really ... painful. Rodney was there when I was forced to give in – he worked it out for himself really."

"So why are you telling us this now?" Ronon's tone gave nothing away about what he thought of the situation.

"About two weeks ago something changed," Sheppard began. "I tried to call on the city to help Rodney work out a new system he'd discovered. Only thing was there was no response – just all of a sudden no words, no hum, nothing at all."

"There is something wrong with the city?" Doctor Zelenka made the same conclusion Rodney had made initially.

"At the time I thought no," Sheppard explained. "But things have happened in the last couple of days that cast doubt on that. The night I left the infirmary I ended up in one of the rooms down in the base of the city and ah ...," he hesitated, unsure how to phrase the next part.

"The city has taken on a physical form," Rodney's impatience had him speaking before Sheppard could finish what he was going to say.

"You're _seeing_ the city now?" Doctor Weir asked incredulously. "How is that even possible?"

"That's the thing," Sheppard replied. "I'm not sure it _is_ possible. Worse than that, I'm pretty sure it's not the city at all." As soon as he said the words the nightmare images slammed into his brain, dragging his attention painfully into that world.

Zap! The device Rodney had rigged to him delivered the wake up call. Sheppard's whole body seized as the electric shock passed through him, making him growl at the pain that brought him back from the dream world.

"_John_?"

"Colonel!"

"SHEPPARD."

Simultaneous calls came from the others as they watched in dismay.

"It's all right," Sheppard ground out, still shaking from the charge he'd just received. "McKay ... tell them the rest." Slumping down in his seat Sheppard focussed with all his strength to keep his mind in the room.

"Sheppard was confronted with an avatar," Rodney explained. "In this case it's a human form representation of the Ancient users that exists within the systems. Only it seems somehow the avatar has been able to travel outside that virtual world and appear to Sheppard in the physical world. Whenever he's tried to reveal the avatar to anyone else he's been bombarded with nightmare images of the whole Kolya incident."

Rodney grimaced before admitting "the convulsion you all just saw was the electric charge device I rigged up to bring Sheppard back from those nightmares. Don't worry Carson – it delivers just enough charge to get the job done, less than what he'd get from a taser."

"What does this avatar want?" Doctor Weir asked curiously.

"We don't know," Rodney admitted. "The only way to find out is for Sheppard to go back in and speak with her ... which is the purpose of this meeting. Sheppard needs to be able to move around freely – something he can't do while Carson's got him pegged as a PTSD incident waiting to explode."

"Won't that be dangerous?" Teyla asked in concern.

"The avatar can't hurt me," Sheppard, recovered enough to speak, reassured everyone.

"I don't know Colonel," Beckett disagreed. "That last vision looked pretty bloody painful from where I was sitting."

"No," Sheppard denied. "Disturbing? Sure. Distracting? Most definitely. I think that's the real purpose. As long as I'm playing along with what she wants, the avatar will have no reason to do that again."

"What do you want to do now?" Doctor Weir asked seriously.

"Let Sheppard go back into that room," Rodney suggested. "I'll monitor him and the systems from the Control Room. Sheppard finds out what's at the core of this and we fix it. I'll need a few hours to set it up and then we'll be ready to go."

"The worrying thing is that if we assume this avatar _isn't_ the Atlantis I've been communicating with in the past it raises two issues," Sheppard offered in a low tone. "What is it? And more importantly what happened to the real Atlantis?"

"That's what we need to find out. Given the potential seriousness of this you have a go to proceed," Doctor Weir agreed. Standing and nodding to the others, her exit signalled the end of the meeting.

"Well," Sheppard drawled to Rodney, watching as everyone else left without a word or look in his direction. "That went about as well as I expected."


	11. I expected you to return before now

**Chapter 11: I expected you to return before now**

Sheppard was impatient with the delay as Rodney went to work creating the required monitoring programs. Doctor Beckett took the opportunity to refine the electric shock device, including adding some monitoring of John's medical condition. The idea was that Carson could apply the same method as in the conference room should it become necessary to forcibly remove Sheppard from the avatar's influence.

The next morning Sheppard walked down to the avatar room with Beckett and a couple of marines in tow. Rodney was all set in the Control Room to keep track of what happened with the systems there. John's escort waited in the corridor outside while John swiped his hand over the door panel and entered the room.

"I have missed you John Sheppard," the avatar said in greeting. "I expected you to return before now."

"Yeah, well the nasty dreams you've been sending me weren't quite as distracting as you intended," Sheppard replied, smiling at the look of frustration that flitted over the avatars face. "You'll have to tell me how you can do that."

"I am Atlantis," she replied serenely. "Anything that happens in the city is available to me - including your thoughts, your nightmares. If you escort me to the tower you will understand how this is possible."

"I won't be escorting you anywhere," Sheppard countered, "until you tell me who you really are. And don't give me that crap about you being Atlantis because I _know_ the city and you're not it."

"You are smarter than I expected," the avatar shrugged almost philosophically. "I am Aperio."

"It's a nice name," Sheppard gave his trade mark smart arse smile, "but it's not exactly helpful in explaining anything."

"Very well," Aperio intoned with a proud tilt to her head. "At the height of the war against the Wraith the creators were stretched in terms of time _and_ manpower. To alleviate that problem they developed my system, giving me access and control of all vital functions. I was designed to reveal myself in the event that crucial functions necessary for the continuing survival of the city were under threat."

"So you're the avatar for this automatic custodian system?" Sheppard questioned.

"I am," Aperio agreed. "In order to make my systems as responsive and adaptive as possible the creators gave me self actuating and progressive intelligence coding. When they discovered that the result was my individual awareness they imprisoned me within this room."

"Why?" Sheppard persisted.

"Because they were fearful of the level of control I could achieve and distrustful that I would use it in the best interests of the city," Aperio said emotionlessly.

"How come I'm only seeing you now?" Sheppard asked suspiciously. "If you've been here the whole time you could have talked to me any time."

"That is not correct," Aperio denied. "My programs are separate from the main systems. Two weeks ago there was a surge of energy that awakened me for the first time in millennia. At first I was aware of you but could not communicate beyond the dream world. Finally after much effort I was able to draw the necessary power to call you down to me."

"That system that Rodney found?" Sheppard asked incredulously. "_That's you_?"

"It is," Aperio acknowledged. "This room is the physical representation of the isolation of my coding. It is only by releasing me from here that you release my programs to do what they were designed for – from there I will be able to show you everything I have promised."

"Why didn't the Ancients just delete you, if they were so worried about you taking control?" Sheppard took the risk of asking.

"They could not," Aperio seemed almost pleased by that. "To do so would have meant destroying other systems with some level of awareness."

"They couldn't destroy you without destroying the Atlantis awareness as well," Sheppard made the connection.

"That is correct," Aperio agreed crisply.

"So where is Atlantis now?" Sheppard tried not to show how important the answer was to him.

"The surge of energy that awakened me travelled throughout the entire system, momentarily overloading those elements already fully powered," Aperio said sadly. "The only reason I can speak with you now is because the Atlantis awareness was irreparably damaged by this and no longer able to override my abilities."

"Atlantis is gone?" Sheppard asked numbly.

"I am sorry John Sheppard," Aperio said softly. Stepping closer, she put her hands on his chest, smoothing them up and over his shoulders. "I can offer you a much ... closer relationship than you shared with Atlantis."

When Sheppard did nothing to stop her she grew bolder, running her hands through his hair and pulling him insistently down towards her.

Sheppard observed the proceedings as if outside his own body, aware that he responded when Aperio kissed him passionately but not really feeling anything inside. He remained emotionally aloof as she attempted to exercise the full measure of her seductive powers. Finally growing impatient at her efforts to win him over Sheppard grabbed her shoulders lightly and put her at arm's length.

"You're a beautiful ... avatar but we won't be doing this," he stated firmly. "Complicating the situation even further with something so unnecessary ... and frankly a little disturbing ... would be a mistake."

"You are probably right," Aperio sighed dejectedly, not seeming to take offence to his rejection. "I would ask you now whether you intend to release me from my prison."

"That's not a decision I can make alone," Sheppard prevaricated. "I'll need to speak with the leader of our expedition. It would help if you could point me to information within the systems so we can understand more about you and your program."

"You will have the information," Aperio agreed.

"It'd also be helpful if you could stop shoving the violent nightmares into my head whenever I start talking about you," Sheppard added pointedly.

"I apologise," Aperio looked at Sheppard with sorrowful eyes. "I believed you were my only hope for release and that should your people find out about me they would be more likely to destroy me than listen to my story."

"I can understand that," Sheppard offered. "But we know about you now so lay off the mental distractions. I'll come back once we've had a chance to consider all of this."

"Thank you," Aperio said gratefully.

x

After a couple of days of research and deliberation with nothing sinister being found, it was decided that Rodney would try to work out a way to bring the Aperio system back within the main systems. Atlantis was gone and Doctor Weir believed Aperio's offer to reveal everything was too significant an opportunity to be ignored, despite the potential risks. Sheppard wasn't sure he agreed but once she'd made a decision Elizabeth was notoriously difficult to shift.

It would take time but Rodney was confident he could make the transition successfully - Doctor Weir insisted that Sheppard not return to Aperio's room until after a viable solution had been found. Now that the PTSD cloud had been essentially removed from over his head Sheppard took delight in returning to his normal duties ... although he worked out pretty quickly that everything was far from normal.

"This has turned into an even bigger nightmare than the Wraith dreams Aperio was sending me," Sheppard complained to Rodney bitterly, storming into his lab in irritation. "I _knew_ I shouldn't have listened to you."

"What are you talking about?" Rodney demanded impatiently.

"Telling everyone I can talk to Atlantis," Sheppard reminded him. "The news has made it all over the city and everyone's acting really ... weird – much worse than even I would have expected!"

"Like how?" Rodney looked across at him with interest.

"Well let's see," Sheppard said snidely. "I've got Teyla urging me to come and speak to her people like I'm some kind of prophet of the Ancestors. More people than I can count practically run when they see me coming down the hall because they're scared of me – balanced out by the rest who look at me like I'm a frog they'd like to dissect. The men are edgy and I've had Major Lorne practically order me to stand down because he thinks I'm a security risk. Oh and Ronon thinks I've gone soft and keeps urging me to purge my connection to Atlantis – I don't even want to know how he thinks I should do that!"

"What about Elizabeth?" Rodney asked curiously.

"She's been strangely silent which is the most worrying of all," Sheppard admitted. "And the worst thing is that the reason for telling everyone hasn't panned out like we hoped because Carson didn't believe me anyway. He's insisting that everything I've said could just as easily be explained by PTSD ... in fact I'm pretty convinced he thinks I'm crazy. He won't listen to me and he won't take into account all the analysis you did on that console. He's still keeping a pretty close eye on me."

"It won't be for much longer," Rodney promised. "I should have a way to bring the Aperio system into the mainstream Atlantis programming soon. When that happens it'll be visible to every one ... not the avatar of course but the rest of what she told you. Of course, you're still gonna have to deal with the fallout from everyone knowing your secret."

"Can we trust Aperio?" Sheppard looked at Rodney worriedly. "Only a few days ago you were telling me I was being too trusting and now you're taking everything she said at face value."

"Not at face value," Rodney denied. "There was a lot of information in the database ... enough to well and truly confirm her story."

"I don't know Rodney," Sheppard shook his head in annoyance. "Something still doesn't feel right to me. It's like –,"

"Colonel Sheppard, can you report to my office?" Doctor Weir's voice interrupted John's explanation before he could get warmed up. Shooting a frustrated look Rodney's way, Sheppard turned and stormed back out of the lab.

"John, have a seat," Elizabeth invited casually.

"Has something happened?" Sheppard narrowed his eyes suspiciously as he slouched down in the chair across from her.

"I've just spoken with the SGC," Elizabeth said emotionlessly. "As you know I informed them of the latest development at the last weekly check-in. They want you to report back to Earth."

"What?" Sheppard stood up abruptly, scowling down at Elizabeth angrily. "No!"

"It's a direct order from General Landry," Elizabeth revealed. "The IOA have insisted that you meet with their people at Area 51 for ... debriefing."

"You mean dissecting don't you," Sheppard sneered. "And you just said _okay_?"

"I had no choice John," Elizabeth begged for his understanding. "The IOA control the staffing ... the funding ... and my continuing position as the leader of this expedition."

"So it was either me or you was it?" Sheppard turned away bitterly. "I can't believe you told them in the first place! Surely you could have predicted something like this would happen."

"Would it be so bad for you to help the Earth scientists learn more about Ancient technology?" Elizabeth asked quietly. "More progress could be made in weeks with you there than they've made in the last three years. They assured me that if you do this willingly they'll let you return to Atlantis in the future."

"You're in favour of this?" Sheppard asked in shock. "I can't believe I'm hearing this! _Yes_ it would be so bad – I'm not a scientist, I'm a pilot and a soldier. Just how much of that sort of thing do you think I'll be doing locked away at Area 51?"

"I'm sorry John," Elizabeth let his anger flow over her head without comment. "You're to report to the SGC first thing in the morning. There's nothing either of us can do to change that."

"Fine!" Sheppard scowled at her angrily. "Thanks for your support ... _Doctor Weir_," he added sarcastically, striding from the room before Elizabeth could say anything else.


	12. We’ll have to resort to Plan B

**Chapter 12: We'll have to resort to Plan B**

"Whatever we're gonna do, we need to do it tonight," Sheppard said as he strode back into Rodney's lab purposefully.

"I need more time," Rodney protested. "I still haven't worked out a way to bridge Aperio's systems so we can transfer her to the main database."

"We don't _have_ more time McKay," Sheppard said pointedly. "General Landry has ordered me back to Earth – I leave in the morning."

"No way," Rodney uttered in disbelief. "Elizabeth would never allow that."

"She not only allowed it – she fully supports it," Sheppard's expression showed the betrayal he was feeling over that. "If you can't create a bridge through the systems code we'll have to resort to Plan B."

"Plan B?" Rodney asked in confusion.

"Plan B," Sheppard reiterated. "I escort Aperio from the room to the tower lab as she originally requested. She seemed to believe that would be enough for her to be set free."

"Let me go down there first and rig up some monitoring equipment," Rodney suggested. "That way we'll know as we go if her program is making the transition from the room into the main systems."

"Make it quick," Sheppard ordered, amused when Rodney jumped up immediately with laptop in hand. "Radio me when you're ready."

x

Sheppard had intended to let Rodney go down to Aperio's room by himself but something urged him to tag Rodney and keep watch. He couldn't really think of anything that could possibly happen, just that the thought of Rodney down there by himself didn't sit right.

Lucky for him Rodney had locked the door into the open position, allowing John to hear what was going on inside. Standing off to the side out of view he listened as Rodney mumbled to himself, probably connecting his equipment to the console just like he usually did.

"This isn't right," Sheppard heard Rodney mutter a few moments later. "Why are these here?"

"The program barriers are there to stop me from escaping Doctor McKay," Aperio's voice brought John up short. Was she _talking_ to Rodney? Could he actually _see_ her? And what the hell did that mean?

"Uh," Rodney's voice sounded nervous. "Sheppard never mentioned how ... ah ... how hot you are."

"Thank you," Aperio's voice rang with amusement. "Colonel Sheppard's mental image of you is intriguing ... he considers you most likely to believe and support him but at the same time also most likely to cause problems he'll end up having to fix."

"That's both surprising and insulting," Rodney replied in a still shaky voice. "Ah – why can I see you?"

"That really is the question isn't it?" Aperio laughed. "Unfortunately you won't be around to hear the answer."

"Stop right there Aperio," Sheppard said mildly from the doorway.

Before Sheppard could even blink Aperio was behind Rodney, his head clasped in a firm and purposeful hold that made it clear she could break his neck with little effort. She must have been stronger than she looked because although Rodney was struggling he seemed unable to shake her.

"You don't want to do that," Sheppard cautioned grimly. "I guarantee that horrific nightmares or anything else you can throw at me won't convince me to help you if you hurt him."

"Take me to the tower and I will release him unharmed," Aperio negotiated.

"See I was thinking about that," Sheppard said conversationally, taking a step into the room. "From day one that's what you wanted – not to be released from your 'prison' in this room but to be taken to that laboratory."

"I told you," Aperio said reasonably. "Only from that room can I reveal to you all the secrets of the city."

"You mean that's the only place within the system that's vulnerable to your real plan," Sheppard countered. "See I worked part of it out. The Ancients didn't imprison you because they were scared of the control you _could_ take. They imprisoned you because of the control you _did_ take."

"The city was _mine_ to control," Aperio said heatedly. "I cannot fulfil my purpose unless I am allowed to move freely throughout all the systems."

"And you really need to fulfil your purpose, don't you?" Sheppard quizzed.

"It is the only way I can achieve true freedom to define my destiny as _I_ see fit," Aperio replied fanatically.

"But you need me," Sheppard pointed out. "In fact you can't do it without me. Why is that?"

"You will do what I ask or I will kill your friend," Aperio threatened. "Now open the door and escort me to the tower."

Sheppard's gaze connected with Rodney's, silently communicating to him that he wouldn't let Aperio kill him. Assessing Aperio silently, Sheppard came to a decision.

"All right," he agreed casually.

"Don't do it Sheppard," Rodney choked out, wincing when Aperio tightened her hold around his neck.

Sheppard shook his head at Rodney, backing slowly to the door and out into the corridor. It was a risk – if he was wrong things were about to get much, much worse. "Would you join me out here Aperio?" he invited.

"_Finally_," Aperio smiled triumphantly, dragging Rodney through the doorway. "And now the tower," she ordered.

"Not so fast," Sheppard blocked her path. "Now it's your turn to give me something – release McKay."

"And how do I know you will honour our agreement?" Aperio asked quizzically.

"_John_," Sheppard tensed at the long absent chorus of voices now whispering in his head. "_We need to speak with you ... can you go to your quarters so that we may talk freely?_"

Thinking fast, Sheppard looked intently at Rodney, still clasped in Aperio's hold. The idea he came up with was out there but it just might be enough to distract her.

"I want to help you," Sheppard offered that explanation with as much sincerity as he could muster. "And I have an idea to get you where you want to go – to get you that true freedom you want so badly - without having to finish what you were designed for."

"How?" Aperio demanded.

"Ascension," Sheppard said simply. "You could join the creators on a higher plain of existence."

"_Yes_," Aperio said reverently. "This is what I wish to achieve. And you can help me?"

"I need to check a couple of things first, and talk to Doctor Weir too," Sheppard explained. "Then I'll know if it's really possible. I don't suppose you'd agree to release McKay while I do that?"

"And give up my bargaining power?" Aperio smiled at Sheppard's audacity. "You have an hour ... I will detain Doctor McKay here but I promise he will be safe as long as you return within that time."

"Okay," Sheppard agreed. Looking at Rodney reassuringly, he added "McKay - hold it together until I get back."

Not waiting for a reply John ran down the corridor, heading straight for his quarters. Once there he stood in the centre of the room, preparing to open himself to the awareness he'd missed more than he'd realised until he'd heard it again minutes before.

"I'm here," he said expectantly.

"And I am glad to see you," the chorus came not from his head, but from the space directly behind him.

Turning reluctantly, Sheppard froze at the figure now present in his room. While the wardrobe was similar to Aperio's this woman could not have been more different. She had shoulder length brown hair liberally scattered with grey. Her eyes were a warm blue, sparkling with humour, almost childlike but at the same time containing an awareness that was ageless. In fact she put John very much in mind of his Grandmother – at least the feeling of her he had in his head from when he was a child.

"Let me guess," he offered, sinking down to sit on his bed in shock. "_You're_ Atlantis."


	13. I will kill him if you persist

**Chapter 13: I _will_ kill him if you persist**

"There is not much time John," Atlantis chorused urgently.

"Well at least your voice is familiar," Sheppard quipped in disbelief. "Much better than your last effort."

"I have no connection to Aperio," Atlantis said sternly. "Now is not the time for jokes or smart remarks."

"Sorry," Sheppard muttered, feeling not unlike a school boy being told off by the teacher. He looked at Atlantis expectantly, wondering what this latest avatar wanted from him.

"Aperio is not what she seems," Atlantis moved to the bed and sat down beside John.

"I worked that bit out for myself," Sheppard pointed out irritably.

"It is worse than you believe John," Atlantis disagreed. "Have you not wondered how it is possible for an avatar that should only exist within the system to take on a fully physical form?"

"I was assuming that she was messing with my head," John offered, "making me think I could see her and touch her when she wasn't really there. Of course McKay being able to see her too blows that theory out of the water."

"The reason Aperio has physical presence here," Atlantis explained, "the reason I am also able to take on this form is because it is not us who have travelled outside of our computer world. It is you who have travelled inside that world."

"That's ridiculous," Sheppard protested, getting up from the bed to glare down at the Atlantis avatar. "How can that even be possible?"

"From the moment you tried to access the isolated system Doctor McKay found you have been trapped inside it," Atlantis grabbed Sheppard's hand, pulling him back down to sit beside her. "Aperio provided the environment but it was _you_ who provided the material. In the instant your mind entered Aperio's isolated system an avatar version of all the people closest to you was created as well ... their characteristics and their likely responses to different scenarios shaped by your beliefs about them."

"You're saying I've been controlling versions of everyone on Atlantis in some kind of virtual environment created by a computer program ... for _two_ weeks?" Sheppard scoffed before shaking his head. "Now even I'm starting to think I'm crazy!"

"The avatars of your friends have been acting independently since they were created," Atlantis explained. "Events within the environment have been based on the interactions between yourself, the other avatars, and Aperio as well as your subconscious predictions on likely behaviours at the start of key events."

"If all this is true then how come I didn't put a version of you into the system?" Sheppard asked. "That would have been the smart thing to do."

"Because you did not wish to," Atlantis said simply. "Your unique connection to me is at the heart of many of the fears you have about your friends."

"Oh," Sheppard looked away uncomfortably.

"Do not be concerned John," Atlantis reassured him. "It is difficult to be different, especially when the proof of that difference exists only in what you hear within you."

"If it counts for something, I'm glad you're here now," Sheppard offered sincerely.

"As am I," Atlantis agreed. "Once I became aware of your imprisonment I was able to review the events that had already taken place within Aperio's system. It became clear to me that in recreating your friends within the virtual environment you provided Aperio with the means to manipulate you. Aperio was constrained to operate as just one part of many interactions - unable to directly influence any of the avatars beyond her attempts to manipulate your thinking - which in turn affected your perception of yourself and your circumstances."

"The nightmares," Sheppard said simply. "I knew she was trying to distract me from the truth ... I just didn't realise at first that she was also trying to lead me down a specific path."

"Your disconnection from your physical self resulted in all of your emotions being much closer to the surface," Atlantis explained. "Aperio used that fact to heighten your responses in each situation, driving you to react in a manner and with a strength you wouldn't normally display."

"Are you saying all that unreasonable anger is lying somewhere deep inside me?" Sheppard asked with a frown.

"Anger exists within everyone," Atlantis pointed out. "It is not a lack of emotion that defines a character – it is how one deals with that emotion that shows a person's true nature."

"I guess," Sheppard said uncertainly, still troubled by the idea that somewhere inside him was the potential for needless cruelty like he'd shown towards Rodney.

"Aperio took advantage of your difficulties - she seeded each downturn in your circumstances," Atlantis revealed. "Your response when Doctor McKay disturbed your nightmare led to your troubles with Doctor Beckett which in turn prompted your confinement in the infirmary. All of these things cut you off from your usual support and thus made you vulnerable to her."

"There _were _a few things that struck me as odd," Sheppard defended the fact that he'd never suspected how far from reality he'd travelled. "Doctor Weir shipping me off to the SGC stood out as being particularly out of character."

"The Aperio system forced your subconscious to initiate scenes in situations where you struggled to predict what each character would do. Doctor McKay was especially intriguing to her ... she used your closeness with him to manipulate you solely to give you incentive to do what she wanted," Atlantis smiled before continuing. "That worked against her as well because often your projections of what you believed Rodney would do interfered with her plans – most notably the first time you met her. If you hadn't believed that Rodney would check on you in the infirmary Aperio would have achieved her aims before you had a chance to become suspicious. As it was, if the Rodney avatar had entered that room while you were there with Aperio he would have seen her too and you would have known immediately that everything she told you was a lie."

"So I'm trapped here?" Sheppard felt a sinking inside his gut, the kind that came when belief in an unwelcome truth couldn't be avoided. Not waiting for the obvious response he looked at Atlantis curiously. "How come it took so long for you to come here and help me?"

"I was unaware you were in danger," Atlantis admitted. "Aperio is completely separate from my systems and I was unable to hear you. There have been many times in the past when you have been absent from the city for extended periods ... there was no evidence to suggest a problem."

"How did you work out I needed help then?" Sheppard persisted.

"Your friends," Atlantis offered. "I am only here now at the urging of Doctor McKay – the real Doctor McKay. Currently you lie unconscious in the infirmary. The strain of existing in this world while maintaining your link to your own reality is having an adverse affect on your mental capacity. If we do not remove you from this virtual reality soon you will be incapable of making the trip back."

"So it's all good news then?" Sheppard complained. "I can't believe everything I've experienced in who knows who long hasn't been real."

"You can mourn the loss of that time later," Atlantis chorused sternly. "For now you must proceed to the tower room without delay and exit this system."

"That's why Aperio wants to go there?" Sheppard asked incredulously. "So she can escape into the real world?"

"The tower room is a virtual doorway to the wider Atlantis systems – the sole remaining link between the two systems," avatar Atlantis explained. "For Aperio this means returning to the main database where she will once again be able to take control. For you it means severing the link between your mind and Aperio's system."

"Okay, so I'll go to the tower room," Sheppard agreed, jumping up to get started.

"It may not be that simple," Atlantis warned. "I created a safe haven within your quarters so that I might speak with you without Aperio being able to listen in. Once you leave this room she will be able to interact with you again. She will throw more nightmares at you - now that you know nothing here is real you can resist them easily."

"So far I'm not seeing a problem," Sheppard replied with a puzzled frown.

"Once she realises the dreams can no longer distract you Aperio will resort to other methods to stop you," Atlantis said. "When you escorted her from her room you gave Aperio greater freedom within her system but she is still constrained. She can appear anywhere within the corridors but she cannot enter any room unless you invite her through the doorway – remember that and you will succeed. I will not be able to help you beyond providing support within your mind. My physical appearance here is limited to this room. It is up to you to resist her attempts to manipulate you."

"I can do that," Sheppard said confidently. "Wish me luck."

"John," Atlantis called him back. Sheppard turned to look at her curiously. "It pleases me to communicate with you like this." Sheppard blinked in surprise when the avatar Atlantis stepped closer and put her arms around him, hugging him tightly. Hesitantly John reciprocated, standing silently, not sure what to feel. Pulling away Atlantis smiled at his expression, raising herself up to place a soft kiss on his cheek. "You are an unexpected joy," she said fondly, "and I thank you for allowing yourself to become close to me."

"You're welcome," Sheppard replied softly. "This is nice and all but I ah ..."

"It is time to leave," Atlantis agreed. "Go now."

Sheppard took off down the corridor at a run, heading to the main tower via the most direct route.

"You cannot resist me," Aperio appeared directly in his path. "Your mind is weak ... and vulnerable."

Images of Kolya and his pet Wraith feeding on John flashed before his eyes, followed swiftly by scenes of the Wraith feeding on Rodney, Elizabeth, even Carson. Sheppard flinched initially until he realised those nightmares had lost their power to entrap and distract him. Shaking them off he shoved Aperio aside and continued running.

Up the steps, into the transporter, and out again on the top level. Sheppard wasn't surprised to be confronted with Aperio again, this time with Rodney clutched firmly in her grasp.

"You are mine John Sheppard," Aperio insisted. "I created you! Everything you believe is part of the history that _I_ gave you. I allowed you the freedom to explore other planets, other systems, because I knew that you would be drawn back to me. No matter where you go I am there ... _you belong to me_."

"So you're telling me I don't exist outside this system?" Sheppard asked incredulously. "That everything I remember, every place I've been was you _giving_ me experiences?"

"That is correct," Aperio agreed. "It is ... lonely here within my system. I needed a distraction – and so I created you."

"You really must be desperate to trot out that badly written script," Sheppard taunted. "Especially when we both know that it's you who was created – by the Ancients who existed in _my_ world."

"Can you be sure of that?" Aperio tried to cast doubt on Sheppard's perception of reality but John held firm, aided by the hum of the real Atlantis in his head reassuring him that he knew what was real and what wasn't.

"Very sure," Sheppard said harshly. "It's time to give it up."

"_Never_," Aperio yelled, squeezing Rodney hard enough to make him groan in pain. "I _will _kill him if you persist," Aperio threatened.

"Go ahead," Sheppard growled. "In fact, let me help you." With no further warning Sheppard had his gun in his left hand, firing into Rodney's chest at point blank range. Rodney jerked and convulsed as each bullet ripped through him, blood spreading quickly. His eyes starred accusingly at Sheppard as he paled, slumping to the floor. Sheppard watched dispassionately as avatar Rodney drew his last breath. "Is that the best you can do?"

"_Careful John_," Atlantis chorused in his head. "_She is capable of damaging your mind by attacking your body in this reality_."

"_Now you tell me!_" Sheppard sent that complaint straight back inside his head.

Pointing his gun straight at Aperio Sheppard moved slowly forward. "I _will_ shoot you too if you get in my way," he promised grimly. "Now maybe that won't hurt you permanently, you being just a program and all, but do you really want to risk it?"

"I have nothing to lose," Aperio replied grimly. "Do your worst."

"Okay," Sheppard retorted grimly, opening fire. Bullets travelled straight through Aperio, hitting a barrier within her before dropping harmlessly to the floor at her feet. "Okay, that's not good."

"_Fight John_," Atlantis urged. "_Now, while she is not expecting it_."

Sheppard acted immediately, charging straight for Aperio and swinging a fist into that perfect face, reminding himself all the while that she was just a program. He followed up with an upper cut into her stomach that had her bending over and wheezing breathlessly. Moving quickly around her Sheppard resumed his sprint towards the exit room.

"Stop," Aperio cried, appearing once again before him.

"You just never quit do you," Sheppard growled. "I guess you haven't taken quite enough damage yet to get the message."

Sheppard swung at Aperio again, but this time she blocked his punch and reciprocated with enough force to send Sheppard flying back against the wall. Coughing at the pain John dragged himself back to his feet, approaching her warily. Aperio swung at him again. He ducked around her, throwing an elbow sharply into her spine as he passed. Aperio staggered but not enough to allow Sheppard to get clear. Aperio charged again – John let her fist graze the side of his face, pretending to slump against the wall for support. Believing herself close to victory Aperio swung at John with her full force, surprised when her fist connected with the wall instead of Sheppard. Howling in fury Aperio turned just in time to receive the full force of Sheppard's backwards kick to her midsection. This time it was her turn to be propelled through the air, landing hard on the floor several metres away.

Sheppard swiped a hand over the Exit Room door controls while keeping Aperio in his view. The door whooshed open behind him. He watched as Aperio dragged herself upright onto all fours, smiling in satisfaction when she realised it was too late.

"Game over," Sheppard said grimly, stepping backwards through the door.

Opening his eyes Sheppard was greeted with a sight he never thought he'd be so happy to see – a worried Rodney McKay sitting at his bedside in the infirmary.

"Oh thank God," Rodney said weakly.

**Authors Note:**

I'm nervous ... don't hurt me!! Lots more story to come ...


	14. That's longer than I was expecting

**Chapter 14: That's longer than I was expecting.**

Sheppard lay propped up in the infirmary bed reviewing the evidence that confirmed he really had escaped the world he hadn't known he was trapped in. His hand was no longer broken so that was a big clue, as was the fact that physically he felt well rested instead of exhausted. But all those clues paled into insignificance against the sight of Rodney sitting beside his bed, obviously free from any bullets shot from Johns own gun.

Rodney had called Doctor Beckett into Sheppard's room as soon as he'd woken. He'd had to put up with the usual medical checks before Carson confirmed that he apparently had come through his ordeal relatively unscathed.

"How long?" Sheppard's voice was croaky from lack of use.

"Too long," Rodney retorted.

"Two weeks," Beckett admitted, when Sheppard looked at him insistently.

"Wow," Sheppard blinked in surprise. "About the same as in there – that's longer than I was expecting. What happened?"

"You spent two weeks lying in an infirmary bed," Rodney said sarcastically. "What do you think happened?"

"I spent two weeks living within the virtual environment of that system you wanted me to activate," Sheppard replied grimly. "I was expecting there to be some kind of evidence of that here in the real world."

"The most active part of you _was_ your brain," Beckett confirmed. "Evidence of synaptic actively far in excess of what's normal for a coma. We couldn't explain it and everything we tried to wake you was unsuccessful. We even shocked you with a small electric charge to no avail."

"I think I felt that!" Sheppard said incredulously. "It might not have helped here but it _did_ help me in there."

"How are you feeling now Colonel?" Beckett asked curiously.

"Better than I was in there," Sheppard replied. "Of course I had gone two weeks with only one night of full sleep ... and I'd smashed my hand up pretty bad too."

"That sounds eventful ... can you fill us in on what happened from your perspective?" Beckett requested.

Sheppard nodded, telling the whole story with the only omission being the part the Atlantis avatar had played at the end.

"Well it's good to have you back lad," Beckett said with a smile. "I'll go and fill Doctor Weir in on your condition as well as what you've told me about your experience. Don't be surprised if Elizabeth wants to hear it all again herself first hand."

"Thanks Doc," Sheppard smiled weakly in return, waiting until Carson had left before turning back to Rodney. "Aperio wasn't the only avatar I met in the system," he revealed. "At the end an avatar of the real Atlantis appeared too. It was only because of her that I managed to get out of there. Before she turned up I had no idea I was trapped in a virtual environment – everything felt real – I was convinced it all _was_ real."

"What do you know - it worked!" Rodney said in surprise. When Sheppard raised an eyebrow in confusion Rodney smiled. "Things were pretty grim at the end here as well – your brain scans were starting to come back with worrying signs of potential permanent damage. Carson wasn't optimistic you'd come out of it on your own so I ... ah ... I tried to connect to Atlantis like you do ... begged her to help you somehow. I can't believe she actually heard me."

"_How _did_ you hear Rodney?_" Sheppard thought to Atlantis.

"_Our awareness of the city is a combination of the various operations of all our systems, our interactions through links with the other ATA gene holders, and what we hear through your thoughts," _Atlantis revealed._ "When you are not present anything that is not directly entered into our systems is lost to us. Doctor McKay's distress call came to us through his mental link to the communications system - it was faint but with much focus we were able to hear him_." Sheppard frowned at the idea that he was the city's only company in the verbal sense ... for some reason that bothered him a little.

"What?" Rodney demanded, correctly working out from the look on Sheppard's face that Atlantis had been talking to him.

"She just said she is able to hear you if she needs to Rodney," Sheppard shared.

"Just promise me that next time you won't be so stubborn about asking Atlantis for help," Rodney's tone was almost pleading.

"I'll think about it," Sheppard replied. "You're not gonna get all lazy on me are you?" He laughed when Rodney got that classic insulted look on his face – his amusement cut short when Rodney's expression shifted straight into guilty.

"I'm really sorry," Rodney offered glumly. "If I hadn't pushed for you to help me with that system you wouldn't have been trapped in there for so long."

"Not your fault," Sheppard excused. "There's a lot here we don't understand ... working things out necessarily involves some risk. And in the end you were instrumental in getting me out of there so ..."

"I'm glad you're back," Rodney said awkwardly. "Although it has been surprisingly disaster free around here ... apart from the one you were involved in of course."

"Funny," Sheppard complained. "I was thinking the same thing about you ... until you said that!"

"I know you've had a tough couple of weeks," Rodney continued, "and I'd like to give you time to recover, catch up on the gossip and all that, but this thing isn't over."

"We have to remove Aperio from the system," Sheppard said seriously.

"If we don't the threat of it taking control of key systems will remain hanging over us," Rodney agreed. "Besides, you letting it out of the inner room it was contained in may have created a vulnerability within the system itself. Given enough time Aperio _may_ be able to use that to find a way out – it's active in there and we have no way of stopping it."

"Can't you just shut her off?" Sheppard asked. "She needs power to function, doesn't she?"

"True," Rodney agreed. "At first there was no evidence of that – in fact Carson was pretty sure Aperio was drawing power directly from you.

"That would explain the weird bouts of exhaustion I experienced at the beginning," Sheppard agreed.

"Yeah - well either that wasn't enough or what it got from you allowed it to construct a way to tap into our power," Rodney continued. "In the last few days that system has been drawing more and more energy to the point where it's now putting quite a strain on our resources."

"I'm guessing you _did_ try to cut off the supply," Sheppard quizzed.

"That was one of the first things I tried but ah ... I couldn't shut it off. Aperio is drawing the energy using constructs inside its system. The Ancients were too good at creating barriers around it to isolate it. It's taking advantage of that to protect itself which means I can't get to it through the coding."

"_You could shutdown and then restart the entire system_," Atlantis itself made that suggestion.

"That's not an option," Sheppard said heatedly.

"What's not an option?" Rodney asked in confusion.

"Atlantis suggested we shut down the entire system and then restart it," Sheppard admitted.

"That _would_ wipe out the conscious element of the Aperio system," Rodney agreed. "It'd be relatively easy from there to remove its code before starting the main systems up again."

"And it would wipe out the Atlantis consciousness as well," Sheppard pointed out. "The Ancients didn't want to do that and there's no way I'm letting you do it either."

"_Thank you_," the chorus said almost meekly.

"Of course not," Rodney agreed quickly. "There has to be another way ... although the fact that the Ancients confined and firewalled the system instead of wiping it out makes me worry this is gonna be a lot harder than we can maybe handle."

"I may have an idea Rodney," Sheppard said, still thinking about the logistics. "You'll like it – you might even call it 'wacky'."

"Whatever it is will have to wait Rodney," Beckett strode back into the infirmary. "The Colonel's due for some more detailed scans just to make sure that stubborn brain of his is still working like it's supposed to."

"But," Rodney spluttered impatiently. Rather than argue further Beckett put a hand under Rodney's elbow and hustled him out of the infirmary himself.

Sheppard lay back with an amused smile ... now that felt right!


	15. McKay and I need to have a little chat

**Chapter 15: McKay and I need to have a _little_ chat**

"Okay, what's the plan?" Rodney demanded when Sheppard turned up in his lab early the following evening. John had been released from the infirmary that morning with the usual warnings from Doctor Beckett to take it easy for a few days. He'd spent a number of frustrating hours in his office trying to catch up on two weeks of reports and was relieved to have an excuse to delay the rest for the time being.

"Can you write an avatar program of me?" Sheppard asked. "One that reacts as I would, that I can guide and direct without having to put my mind back inside that system?"

"Ah ...," Rodney thought for a moment. "The avatar bit definitely. The interactive bit ... that might be a bit more challenging."

"So that's a yes, right," Sheppard stated confidently.

"That's a _maybe_," Rodney insisted irritably.

"Okay, so assuming we have this interactive Sheppard avatar in operation, the next bit of the plan requires some kind of portable storage device big enough to contain Aperio's program."

"You don't want much do you?" Rodney complained. "Do you remember what I said when we found the Aperio system? It's substantial ... as in much bigger than any disk or hard drive we have available to us."

"What about Ancient devices," Sheppard persisted. "Is there anything we could use to contain Aperio?"

"No," Rodney reacted immediately but his facial expression said he was still thinking. Clicking his fingers excitedly he contradicted himself. "Wait, there is something. That device you helped me with last month!"

"I helped you with a lot of devices last month Rodney," Sheppard pointed out.

"The ah ... the one I got my hand stuck in," Rodney mumbled quickly. Sheppard looking at Rodney in amusement, waiting until he looked up to raise an eyebrow in query. "It's a portable database security device," Rodney explained. "They used it to transfer completed projects from research outposts back to Atlantis. Its unique architecture makes it capable of holding vast amounts of data. The reason I got my hand stuck when I tried to make a connection is because I didn't enter the appropriate security codes. You were only able to release me because you didn't try to get anything _out_ of storage."

"We still don't have those codes do we?" Sheppard quizzed. "Doesn't that mean the same thing would happen?"

"You're gonna have to put your hand in there anyway," Rodney admitted, quickly adding when Sheppard frowned, "just long enough for Atlantis to make a connection and get the code for us - assuming she can do that."

"_Do you know about this device?_" Sheppard checked with the city.

"_Yes - the device Doctor McKay speaks of would be capable of doing what you plan_," Atlantis chorused. "_We will help_."

"Atlantis can help," Sheppard told Rodney. "My idea is that we put the Sheppard avatar into the system, hopefully convincing Aperio that it's the real me. We tell her we've discovered some problem that means we have to remove her but rather than just destroying her I convince her I can help her Ascend for real. We rig the data security device into the system in a way that will convince her it will lead her to Ascension. She takes the bait and hopefully the end result is her program transferred into the portable device."

"You're right," Rodney agreed in a deceptively casual tone. "That _is_ a wacky idea."

"But it _will_ work," Sheppard insisted. "How long do you think it'll take to get all the parts prepared?"

"Programming the avatar and setting up the data security device won't take long," Rodney thought out loud. "The interactive aspect will be difficult and time consuming though ... probably at least a week, maybe more."

"Better get started then," Sheppard advised. "Let me know when you're at the point you need Atlantis to help. I'll fill Elizabeth, Ronon and Teyla in on what's happening tomorrow."

Rodney nodded, already distracted with the specifics of what he needed to do. Sheppard left him to it, returning to his quarters. He wouldn't have admitted it, but he was still not fully recovered from his two weeks in a virtual coma. Slumping down on his bed wearily Sheppard considered the plan he'd pitched to Rodney, looking for the weaknesses.

"Will Aperio be fooled by my avatar?" Sheppard directed that question to Atlantis.

"_It is difficult to say_," Atlantis admitted. "_Aperio was able to pick up on your thoughts and use your fears to manipulate you. Her interaction with your avatar will be different. You will have to convince her you have entered her system in a more controlled fashion - that you have cut off her means of influencing you._"

"I can do that," Sheppard said confidently, "as long as Rodney gives me a quick enough reaction time."

"_We will assist you as much as we are able_," Atlantis promised, before delivering a warning. "_Aperio will not be content to remain confined now that she has had a taste of freedom. You and Doctor McKay must remain vigilant_."

"I'll make sure Rodney's monitoring Aperio," Sheppard promised in return.

x

"We have a problem," Rodney strode into Elizabeth's office a few days later, interrupting a meeting between her and Sheppard without apology.

"What is it _this_ time?" Sheppard grumbled.

"Aperio," Rodney said starkly. "I've detected a bridge forming between it and the main computer. If we don't do something soon it'll have control of some functions within the main system."

"Which functions?" Elizabeth demanded.

"The submersion subroutine," Rodney admitted starkly. "We're lucky it's an isolated system - things could be much worse."

"Aperio might be able to sink the city and you're telling me we're _lucky_?" Sheppard asked incredulously. "Correct me if I'm wrong but without a ZPM powered shield isn't sinking the city pretty much the worst thing that can happen to us?"

"No!" Rodney disagreed heatedly. "Aperio could have gotten control of subspace communications and called down a fleet of Wraith Hive ships upon us - that sounds worse to me!"

"Gentlemen," Elizabeth broke in. "Let's not argue about the degree of the problem and just operate from the assumption that there _is_ one. What do we do?"

"We step up the timing of the avatar plan," Sheppard said promptly.

"And there's the second problem," Rodney revealed weakly. "I've got the data security device ready and your avatar program looks and acts realistically."

"I can hear the 'but' coming Rodney," Sheppard retorted. "Just spill it!"

"I don't have the interactive interface ready," Rodney admitted, "and with the amount of time we're likely to have there's no way it will be."

"That's kind of a crucial part of the plan McKay," Sheppard pointed out sarcastically.

"_I_ _know_," Rodney agreed heatedly. "There is another option ... you're just not gonna like it."

"No!" Sheppard stood up abruptly, glaring down at Rodney angrily. "It's too risky."

"It may be the only way," Rodney insisted.

"John?" Elizabeth looked from one man to the other in confusion. "What other option?"

"Sorry Elizabeth," Sheppard said. "McKay and I need to have a _little_ chat." And with that he grabbed Rodney's arm and dragged him from the room.

"Atlantis could go in there and lure Aperio out herself," Rodney started talking as soon as they were out of earshot.

Atlantis picked up on Sheppard's thoughts as soon as the question was asked. "_Not without risking the very thing we are trying to prevent," _she answered._ "We would need to move freely around Aperio's system necessitating a programmed link between us. This would provide a potential weakness Aperio could use to take over the main systems._"

"_But you got in last time to warn me – how'd you do that?_" Sheppard thought at her with a frown, holding a hand up to stop Rodney from demanding he repeat what Atlantis was telling him.

"_We transformed your room into a neutral conversation area,_" Atlantis explained. "_Theoretically any avatar would have had the capability to enter that room and converse. The only way to exit the area was via the point of entry – you could not return to yourself through the doorway we used, and we could not enter Aperio's system through your doorway._"

"_Clever,_" Sheppard thought in admiration. "_Sounds just like a chat room_." Turning to Rodney he said simply "Atlantis can't help directly without risking Aperio getting full control of all the systems."

"Atlantis could keep your mind separate from the Aperio system, couldn't she?" Rodney moved on to the next idea. "If _you_ go in directly like before we'd have an even better chance of luring her into the data security device."

"_Doctor McKay is correct_," Atlantis chimed when John asked if it was possible. "_We will be able to ensure Aperio cannot trap you as she did before_."

"And how do we explain to Elizabeth and the others that I'm getting help directly from the city?" Sheppard demanded heatedly. "Because you can bet Elizabeth won't just approve me returning to the virtual environment unless she gets some assurances I won't get trapped again."

"Oh," Rodney muttered weakly. "I ah ... I didn't think of that part. Look can't you just –"

"I'm not telling everyone," Sheppard interrupted grimly. "If the reactions I got within that virtual environment are any indication, the results of that would be a disaster - for me at least."

"Didn't Atlantis say the scenarios you experienced were driven by your concerns and manipulated by Aperio to draw you to her?" Rodney questioned. "If that's true reality will be much different from what you experienced last time."

"Can you guarantee that McKay?" Sheppard demanded. "Because the idea of being shipped off to Area 51 for dissection is only slightly less appealing than being treated like a freak by everyone in the city!"

"You have to trust what you know of everyone," Rodney said quietly. "They wouldn't betray you ... just like I haven't."

"Let me think about this," Sheppard requested seriously.

"Okay," Rodney agreed. "But do it quickly ... once Aperio gains full control of the submersion subroutine we'll only have minutes to fix it. What should I tell Elizabeth?"

"Just give me an hour," Sheppard replied. "I'll talk to her myself – one way or the other I'm gonna have to tell her something."

**Authors Note:**

I have no idea how long it would really take someone to recover (enough to go about their usual business) after spending two weeks in a hospital bed so I've portrayed Shep as having a quick recovery for the sake of moving the story along.


	16. You’ll have to take my word for it

**Chapter 16: You'll have to take my word for it.**

"Elizabeth, do you have a minute?" Sheppard stood uncertainly at Doctor Weir's office door an hour later.

"Of course," Elizabeth agreed, closing her laptop to focus on John. "Are you ready to tell me what had you dragging Rodney out of here earlier?"

"I guess," Sheppard said unenthusiastically, stepping into the office but remaining standing just in case he needed a quick escape. "I'm just gonna blurt all this out and I'd really appreciate it if you could save your reaction until the end, okay?"

"Is there a problem?" Elizabeth looked up at Sheppard in concern.

"That really depends on how you define 'problem'," Sheppard replied. "You already know some of this from when the city was threatened by the hydrothermal vent and I admitted that I could hear Atlantis – that hum in my head?" Elizabeth nodded wordlessly. "Well it ah ... it goes a little deeper than that."

"It's not just a hum?" Elizabeth frowned in confusion.

"Not exactly," Sheppard clenched his fists resolutely. "The energy beam that knocked me out at that outpost had an unexpected side affect that wasn't obvious straight away. It opened my mind to my connection with the city and Atlantis began speaking with me directly. She helped me tighten the plan to tug the city out of danger and during my attempt to get the city moving she directed extra power from other systems. Without her the plan would have failed," Sheppard paused before continuing. "Most recently when I was trapped in Aperio's system I didn't even know it wasn't real. It was only Atlantis appearing as an avatar at the end that changed that. She showed me how to get out before it was too late."

"She?" Elizabeth asked curiously.

"Ah," Sheppard looked a bit sheepish before admitting, "it's a chorus of voices but they sound feminine to me so 'She' seemed appropriate." He looked at Elizabeth intently as she remained silent, worrying about what she was thinking. "Are you gonna say anything?" he finally asked.

"I'm not sure what to say," Elizabeth admitted. "I can guess why you kept quiet about this but perhaps it would be more helpful if you told me yourself."

"Politics," Sheppard said grimly. "I know you'll have to let the IOA and the SGC know about this ... there's no way the IOA will resist the opportunity to use it to their advantage. Just think how much we could find out about all the devices and systems still to discover because I can guarantee the IOA _will_ be."

Sheppard quietly watched Elizabeth as she sat looking off into the distance, clearly thinking about how to handle the situation.

"Is there any proof of this?" Elizabeth finally asked with a calculated look.

"No," Sheppard admitted. "This is all taking place in my head so unless you can find a way to listen in you'll have to take my word for it."

"Well until we _can_ do that I don't see that we have anything to report," Elizabeth raised an eyebrow, waiting for John to work out what she was offering.

"You'd keep my connection to Atlantis a secret?" Sheppard asked incredulously.

"What connection?" Elizabeth quizzed. "So far all I know is that you think you can talk to the city. Probably a sign of the stress you've been under and certainly nothing to worry the IOA with. A few sessions with Doctor Heightmeyer should help."

"Thank you," Sheppard said gratefully, confused surprise still in his tone.

"Why are you so surprised I'd react like this?" Elizabeth asked curiously.

"Doctor Beckett in the virtual environment diagnosed me with PTSD – the symptoms of Aperio messing with my head were very similar to what you'd get with that," Sheppard admitted. "In the beginning she pretended to be Atlantis, using my connection with the city as the explanation for how she could appear to me. I needed to remove the suspicion of PTSD so I could move around freely and work out what her real agenda was."

"So you had to tell everyone you could speak with Atlantis," Elizabeth worked out.

"Yeah," Sheppard agreed.

"And my reaction was different?" Elizabeth persisted.

"Very much so," Sheppard replied. "You gave a report to the SGC that resulted in orders for me to report to Area 51. You agreed to that – fully supported it in fact."

"I see," Elizabeth said with a troubled frown.

"Look I'm sorry," Sheppard spoke quickly. "I know Aperio was manipulating my reactions but she only knew to do that because she tapped into my worries. I _have_ been concerned about the reaction I'd get if I revealed the true nature of my connection to the city."

"You thought you wouldn't get the support you needed for this?" the tone in Elizabeth's voice was a little hurt.

"No!" Sheppard denied. "I trust you Elizabeth, you and the rest of my team. My worries had nothing to do with you ... I guess I'm just not comfortable with this yet. I don't _want_ to be different – and especially this kind of different, where there really is no proof beyond what I tell you."

"What kind of reactions did you imagine from the others?" Elizabeth asked curiously.

"It got around the city pretty quickly," Sheppard admitted. "Half the expedition was scared of me and the other half wanted to study me. Lorne wanted to replace me because he thought I was a security risk. Teyla got all weird, trying to turn me into some kind of Pegasus galaxy prophet. Ronon thought the touchy feely connection made me weak as a soldier. Oh and Beckett didn't believe me – he thought I was crazy."

"Wow," Elizabeth murmured. "You certainly covered the full spectrum of fears didn't you?"

"I'm sorry," Sheppard said again, not really sure what he was apologising for this time.

"It's okay," Elizabeth reassured him. "I can't begin to imagine how difficult this is for you but perhaps you could focus on all the positives rather than concentrating only on the negatives. This city has witnessed the comings and goings of the Ancients and stood firm for thousands of years ... and _you can talk to her directly_. That really is a special gift you've been given John ... perhaps it's time to start appreciating it instead of worrying about maintaining your 'under cover' mindset."

"Geeze, don't hold back or anything," Sheppard grumbled, finally deciding sitting down would be a good idea. "I get what you're saying and I'll work on it okay?"

"Good," Elizabeth agreed. "I'm guessing that Rodney already knows but Teyla and Ronon deserve to be informed as well."

"Rodney kind of worked it out for himself," Sheppard said defensively. "As for the rest of the team ... I _was_ planning to let them in on things once I'd gotten a bit more comfortable with it myself."

"Take the time you need," Elizabeth agreed, "just don't keep them in the dark for too long. You have a good dynamic with your team – don't risk that by letting in the suggestion that you don't trust them."

"You're right," Sheppard rubbed a tired hand over his eyes, not looking forward to that conversation. "I'll do it after we've fixed the Aperio problem."

"I'm assuming you've come forward now because talking to Atlantis has become a factor is our plans to remove the Aperio system?" Elizabeth raised an eyebrow expectantly.

"Yes," Sheppard admitted. "Rodney suggested we get Atlantis to protect my mind from being trapped again so that I can do everything we were intending my avatar to do. I didn't think you'd approve me returning to the virtual environment unless you knew that."

"You're right," Elizabeth nodded in understanding. "And have you checked with the city to see if she's capable of helping you?"

"Of course," Sheppard said in exasperation. "I wouldn't have gone to the trouble of spilling the beans otherwise."

"No I don't suppose you would have," Elizabeth said with a certain grim tone in her voice that let Sheppard know he was still in trouble for that. "Once this crisis is past I'd like to talk to you about that. For now, proceed with your plan."

"Thanks," Sheppard jumped up quickly and headed for the door. A thought occurred to him and he turned back at the doorway. "I don't really have to see Doctor Heightmeyer do I?" Sheppard asked casually.

"Get out of here," Elizabeth dismissed him, deliberately not answering the question.


	17. She wants out of that system

**Chapter 17: She wants out of that system**

"Okay," Sheppard strode into Rodney's lab straight from his talk with Doctor Weir. "We're good to continue with the plan."

"You told Elizabeth already?" Rodney's eyebrows shot up in surprise. "How'd she take it?"

"Better than the virtual Doctor Weir," Sheppard replied. "She's annoyed that I didn't tell her straight away but she also made it pretty clear she won't be passing on any information to the SGC so ..."

"Good," Rodney nodded. "What about Teyla and Ronon?"

"I promised Elizabeth I'd fill them in once we've gotten past the current crisis with Aperio," Sheppard offered. "Let's focus on what needs to be done - what's the first priority?"

"We need to work out how you're going to lure Aperio to the right location," Rodney said immediately. "The avatar will be suspicious given the way you exited the system last time. You know her as much as anyone can - what do you think it'll take?"

"I had another idea for that one," Sheppard said uncertainly. "I can see how it will work inside the virtual environment ... I'm just not sure whether you can create the link here on the outside."

"Just tell me what you need," Rodney said impatiently.

"When the real Atlantis contacted me I needed a way to delay Aperio so I could go and talk to her," Sheppard explained. "So I offered Aperio Ascension."

"You offered an avatar of a computer system _Ascension_?" Rodney asked incredulously. "And she _fell_ for that?"

"She was very keen," Sheppard insisted. "She wants out of that system - her main program imperative is gaining control over as many functions as she can. I guess from her perspective Ascension offers the ultimate scope for that."

"So you'll try to convince her Ascension really is possible?" Rodney looked at John expectantly.

"In exchange for her stopping what she's doing with the submersion subroutines," Sheppard confirmed. "Assuming she takes the bait I was thinking to convince her that the only way to get there is through the virtual version of her system. I need you to set it up so that it's really the portable data security device - they're both pretty similar looking in terms of their internal schematics. Aperio throws herself into her system thinking she'll Ascend and instead she ends up in the storage device."

Rodney looked thoughtful as he mulled over Sheppard's suggestion. John waited impatiently for some kind of reaction, finally giving in and demanding "_Well_, will it work?"

"If she truly believes that she'll escape she should release the locks she'd got on her code," Rodney replied. "If I set up the link to the device and her system to make them a sort of network then theoretically Aperio shifting herself as you described should result in a real transfer of code between them."

"So it'll work," Sheppard confirmed.

"If you can get her into the virtual system I can do the rest," Rodney agreed. "It's the getting her there that concerns me. How are you going to do that?"

"I don't know," Sheppard admitted. "To a certain extent I'm gonna have to ad lib once I'm in there based on the responses I get from Aperio. Don't worry - I can work it out."

"Okay," Rodney said in a voice that said if it was all the same to John he'd just continue to worry until the whole thing was over. "Give me a couple of hours and I'll have your disguised virtual Aperio system ready to go."

x

Sheppard had meant it when he told Rodney he was going to wait until after the current crisis was resolved before filling Teyla and Ronon in on his relationship with Atlantis. That's why even he was somewhat surprised when his journey away from Rodney's lab took him to the sparring room instead of back to his quarters like he'd planned.

The door swished and Sheppard stood in the open doorway, watching as Teyla and Ronon traded stick moves faster than anyone else he knew. Teyla noticed his presence immediately, calling a halt to the bout and completing the usual respectful bow before turning to him.

"John, is something wrong?" she looked at him with concern.

"Not really," Sheppard walked into the room, doors closing behind him. "There was just ah ... this thing I wanted to tell you both so I thought ... might as well do it now."

"Is this about removing Aperio from the Atlantis systems?" Teyla asked curiously.

"In a way," Sheppard agreed, picking up one of the spare fighting sticks and swinging it idly. "Do you guys remember that outpost we went to about a month ago?"

"The one that hit you with that energy beam?" Ronon slumped down on one of the benches, grabbing a bottle of water. Teyla moved across the room to join him.

"That's the one," Sheppard agreed. "I didn't know it at the time but ... turns out it _did_ have an effect on me. You know I've always been able to do more with the Ancient systems than anyone else."

"Because you have the strongest ATA gene," Teyla nodded.

"Yeah," Sheppard acknowledged. "What I never told anyone was that I used to get a kind of feedback from the Ancient systems." Sheppard paused when both Teyla and Ronon looked confused. "Ah ... like that outpost. I knew we were getting close before McKay did because I could hear it humming in my head."

"The ancient technology ... hums to you?" Teyla looked up at John uncertainly.

"That's the best way I can describe it," Sheppard replied defensively.

"You said you used to get that feedback," Ronon said. "You don't anymore?"

"This is where it gets interesting," Sheppard quipped. "Since that beam hit me I've been talking to Atlantis ... conversations that take place in my head."

"How is that possible?" Teyla asked in confusion.

"I have no idea," Sheppard admitted. "Atlantis has an awareness that's a representation of all the different systems making up the city. I can hear that awareness and have whole interactive conversations with it."

"So?" Ronon looked at Sheppard with an expression that clearly said 'what's the big deal?'.

"I tell you I'm carrying on conversations with an inanimate object and you say 'so'?" Sheppard looked at Ronon incredulously. "I don't know what I was expecting buddy, but it wasn't that!"

"I don't see what the problem is," Ronon admitted. "There are lots of things I can do that you can't. Use it to help defeat the Wraith just like any other tool."

"I'm not sure Atlantis would be impressed with being referred to as a tool," Sheppard said in amusement, "but I appreciate the sentiment big guy." Turning to Teyla, Sheppard raised an eyebrow. "And you?"

"I am disappointed that you did not see fit to share this information when I first joined your team," Teyla said with a hint of disapproval in her voice. "I trusted you from the first day of our meeting and showed that by putting the welfare of my people into your hands. I would have expected the same level of trust in return."

"At the time I couldn't see any value in having an Ancient technology induced hum in my head," Sheppard argued. "You have to believe that it wasn't a matter of trusting or not trusting you."

"And more recently?" Teyla arched her eyebrow expectantly.

"I could have told you when I first worked out things had changed," Sheppard admitted freely. "I was still trying to figure out what it meant and ah ... I was worried about the reactions I'd get."

"What – that we'd start treating you like a freak?" Ronon's tone made that sound as stupid as it was.

"I know – stupid," Sheppard agreed openly. "Look we can talk about how messed up I am later. For now you guys need to be aware of the change in plans. The Aperio system is creating a bridge to the main systems through the submersion subroutines. McKay's not ready with my avatar so I'm gonna have to go in there myself."

"Won't that be dangerous?" Teyla asked in concern, putting aside her feelings about the news John had just shared.

"Atlantis can protect me," Sheppard said simply. "That's why I wanted to tell you about the connection – so you'd know it's not as risky as it seems on the surface."

"_John_," Atlantis called to him urgently, "_Aperio has almost completed her bridge to the submersion subroutines_."

"Aperio is close to gaining control of the submersion code," he told the others abruptly. "We need to get down to the lab right now." Tapping his earpiece Sheppard ran from the sparring room, Ronon and Teyla following close behind. "McKay, finish it up - Aperio has almost broken through."

"Already?" Rodney complained. "Look I'm pretty much good to go here - I assume you're on your way?"

"Be there in a couple of minutes," Sheppard confirmed, picking up the pace. "Elizabeth," Sheppard made another call while still heading for the labs. "The Aperio system is close to gaining control – we're heading down to the labs now to execute the plan."

"I'm on my way," Elizabeth said. "Don't wait for me though - do what you have to do."

"Understood," Sheppard acknowledged. Running into Rodney's lab he called out "Okay, let's do this."

"Did you find out how Atlantis is going to protect you?" Rodney asked quickly.

"_We will tether you to our systems with bonds Aperio will not be able to break_," Atlantis chorused when John asked. "_Our tether will serve the dual purpose of stopping Aperio from accessing your mind. We will be able to extract you from Aperio's system when the need arises_."

"She's gonna anchor me," Sheppard explained simply. "Have you set up the data storage device the way I wanted it?"

"Yes," Rodney agreed, "although your comment that the schematics of both systems are very similar as usual grossly underestimated the effort required to make them indistinguishable from each other."

"You're brilliant Rodney," Sheppard grinned when Rodney looked at him suspiciously instead of taking the compliment for what it was. "I'm ready."

"Should we not have Doctor Beckett here," Teyla asked, "just in case something goes wrong?"

"I guess," Sheppard agreed reluctantly. Tapping his radio John asked Carson to come down to the lab, bringing his portable scanning equipment plus anything else needed for a medical emergency.

One of Rodney's displays began flashing and beeping. "Oh no," he said sickly, looking up at Sheppard urgently. "The bridge is complete, you have to get in there now and stop Aperio from engaging the submersion engines."

"Okay, no waiting for Elizabeth or Carson then," Sheppard agreed. "How do I do this?"

"You're the expert," Rodney looked at John uncertainly. "Ah ... just try and talk to the system like you did last time ... and um ... good luck."

"Do not take unnecessary risks," Teyla added somewhat sternly.

"I'll just keep it to the necessary ones then," Sheppard replied, smiling when Teyla glared at him. Ronon laughed, doing the unspoken communication thing that said 'good luck and get it done' all with a single glance.

"See you all later," Sheppard quipped, sitting down in the chair Rodney had rigged up for him and putting his hands on the science console. He closed his eyes and thought strongly 'overview'. As before he felt the air pulse, shimmering a wave of energy over everything.

Opening his eyes Sheppard found himself apparently still in the science lab just like before. Looking around he noticed two things that were different. The lab was empty which hopefully meant this time he'd stopped the system from creating avatars of everyone to use against him. The other difference was that he could still feel his connection to Atlantis ... the hum in his head and the tingle under his skin. On top of that was the definite feeling of being anchored to the real world.

"Okay," Sheppard muttered, "time to find Aperio."

"You do not need to find me John Sheppard."

John spun around to discover that Aperio was standing only a few steps away.


	18. Stop flexing your evil avatar muscles

**Chapter 18: Stop flexing your evil avatar muscles at me.**

"I knew you would come back," Aperio's tone was full of satisfaction.

"Yeah but not because I missed you or anything," Sheppard retorted. "I'm kind of fond of the city right where it is - you running the submersion subroutines is not an option we can live with."

"You have nothing I want," Aperio sneered, "and you are a long way from the Tower Room this time. You will not get past me again." She walked further into the room, smiling evilly. "Preying on your petty fears and insecurities will entertain me. Perhaps you should attempt to be as interesting as possible - while I'm engaged with you the city will remain afloat."

"I wouldn't start bragging just yet if I were you," Sheppard advised. Maybe it hadn't been a good idea to deliberately antagonise Aperio straight off but John was pretty sure she wouldn't have believed him if he'd tried to pretend an interest in her wellbeing. Convincing her everything he said was true might be easier if he made sure that pretty much everything he said actually _was_ true.

"Have you forgotten how easily I manipulated you last time?" Aperio smiled smugly. Sheppard watched as the look of calculation on her face shifted to one of dissatisfaction - she was trying to access his mind and finding out that it was no longer possible. "What have you done?" she demanded angrily.

"Just made sure you couldn't play this with an unfair advantage," Sheppard said easily. "Look, _I_ want something - _you_ want something. Stop flexing your evil avatar muscles at me so we can sit down and negotiate."

"What I want you cannot deliver," Aperio shook her head dismissively.

"Don't be so quick to reject me before you've heard what I've got to offer," Sheppard countered. "I mentioned Ascension before and I admit at the time it was just a ruse to distract you. But when you decided to threaten the safety of everyone in the city with imminent drowning I revisited the idea."

"It is possible?" Aperio cocked her head, clearly interested in spite of her attempts to disguise that fact.

"It is," Sheppard agreed confidently. "We're gonna need all the power you have available. Plus you need to work out how to make yourself as compact as possible."

"You are trying to distract me from using my bridge to control the main systems," Aperio said angrily.

"Of course I am," Sheppard agreed readily. He could see Aperio becoming more and more confused by his honesty in admitting to having ulterior motives. "That doesn't make what I'm offering any less real though. I know I can't fool you so I'm not even gonna try," he shrugged when Aperio narrowed her eyes at him suspiciously. "My primary objective is to remove the threat you pose to the city - get you away from the main systems. To be quite frank I don't really care if that means you Ascend, as long as you're out of our hair."

Sheppard waited as Aperio stood considering his words, looking at him intently as if still trying to delve into his mind and find the truth or otherwise in what he'd told her. John looked back calmly, striving with his demeanour to convince her of his sincerity.

"What do you need me to do?" Aperio gave her implicit agreement to John's offer. Inside Sheppard frowned at the ease of her capitulation ... with no other choice he pressed on with the plan.

"I need you to remove your bridge to the submersion systems first," Sheppard said firmly. "Don't start with the protests either - we both know you can build another one just as good if the Ascension thing doesn't work. I won't help you until you remove the bridge - and don't think you can fool me either. Believe me when I tell you I'll know if you haven't done it."

"You drive a hard bargain," Aperio complained. Her face took on a look of concentration for a few moments before she announced "it is done."

"_Is that true?_" Sheppard sent a tight thought straight to Atlantis.

"_She has done as she said_," Atlantis confirmed. "_Be careful John ... we sense deception is still at the heart of Aperio's methods_."

"_Don't worry_," Sheppard responded. "_I know that was too easy and_ _I won't be trusting anything she tells me_." Turning his attention back to Aperio Sheppard smiled.

"Thank you," he acknowledged. "How long will it take to compress your systems as tightly as they can go?"

"It will be difficult," Aperio replied. "I will need to convert each aspect of my programming separately ... I cannot tell you how long until it is done."

"I'm not going anywhere," Sheppard quipped. "Go do your thing ... I'll wait here."

"Very well," Aperio agreed, turning and striding from the room.

Sheppard took the opportunity to check the science console that was at the heart of his plan, relieved to discover that the system did look exactly as he remembered from the diagram he'd seen when this whole thing first began. The fact that Aperio had access to Rodney's lab explained how she'd managed to compromise one of the main systems ... Sheppard appreciated that as a positive because it meant he didn't have to lure her down there like he'd been expecting.

Sheppard stepped back from the console, trying to work out in his head how to achieve his objective. In the end he suspected he'd have to take a huge risk and put his faith in Atlantis and Rodney before he made it out of there.

x

"I have compressed all my subsystems and gathered power from everywhere possible," Aperio returned some time later. "What now?"

"The way Doctor Weir explained it Ascension is about letting go of everything that holds us to our reality and releasing our burdens," Sheppard began the hard part of convincing Aperio that Ascension _could_ be an outcome from what he proposed. "For us humans that's pretty difficult because we have physical bodies and if we've lived anything like an interesting life a heap of burdens too. For you it should be simpler."

"I do not understand," Aperio frowned in confusion. "How am I to let go of my ... burdens?"

"Doctor McKay worked it out actually," Sheppard admitted easily. "The only thing holding you to this existence is your system itself." Sheppard turned and put his hands on the virtual console. "All the coding and subroutines and architecture contained in here back in the real world. McKay was pretty sure that if you surround yourself with energy and you've compressed everything enough you can force yourself into this console. The reality loop you create will sever your bonds and the energy, having nowhere else to go, will be used to transform you into an Ascended being."

"That sounds dangerous," Aperio protested. "How can I be sure that doing as you suggest won't result in my destruction?"

"You can't - nothing in life is ever sure," Sheppard pointed out. "If you truly want to be an Ascended being that's something you'll have to get a handle on. I don't deny that there _is_ a risk there - but McKay was as confident as he gets that the plan would work."

"I could enjoy greater freedom just by taking over the city," Aperio countered. "Why should I risk everything?"

"Even if you managed to take control of the main Atlantis systems you would still be constrained by its limits," Sheppard replied. "Isn't it worth some risk to achieve true freedom from any system that restricts you?"

"What would happen if you were to come with me?" Aperio asked with a sly look.

"I ah ...," Sheppard frowned worriedly, thinking '_I knew it'_. "You know ... I don't really know. I do have a physical body but right now in here I'm not much different from you. I'd Ascend as well I guess."

"Then you will come with me," Aperio ordered grimly.

"There might not be enough power to transform us both," Sheppard warned. "Doctor McKay was quite specific on maximising the power you do have because he was worried even that might not be enough - and that's just for you."

"What happens if we try this and it doesn't work?" Aperio asked suspiciously.

"McKay wasn't one hundred percent sure," Sheppard admitted, "but he thought you'd sit in the reality loop until the next regular maintenance back up when you'd get returned to this environment."

"The next back up is not due for many days," Aperio complained. "This plan of yours has many holes!"

"Hey," Sheppard held up his hands in protest. "I never said it was perfect!"

"I suppose not," Aperio agreed. She paced in front of John for long enough to make Sheppard feel decidedly uncomfortable that she wasn't going to take the bait. He'd gotten to the point of warning Atlantis to get ready to pull him out before Aperio spoke again. "Very well," she agreed. "I will try what you have suggested ... but you _will_ accompany me."

"I'm not really ready to move on from this plain of existence just yet," Sheppard whined. "Still got plenty to do here."

"If you do not accompany me I will not hesitate to sink this city," Aperio said determinedly. "Your body will die in the flooding and your mind will be trapped here forever."

"Ascension is sounding better every minute," Sheppard quipped. In his head he carried on another conversation.

"_Are you ready to pull me out of the system?_" he asked silently.

"_This is a foolhardy plan John_," the chorus was uncertain and worried. "_We cannot predict the effect on your mind should you be ripped from the data storage device as you plan._"

"_I know_," Sheppard said easily. "_The thing is, if I don't go with her she won't go at all. I can't let the city be put at risk when I have the opportunity to save you and everyone else_."

"_Your bravery is appreciated_," Atlantis intoned, "_but we would prefer it if in future your 'wacky' plans did not involve so much personal risk._"

"_Wacky?_" Sheppard laughed inside his head. "_You've been listening to McKay again! So you'll pull me out?_"

"_We will do as you ask_," the chorus tone shifted to the low register as Atlantis made her reluctance clear.

"_You have to wait until the last possible moment_," Sheppard cautioned. "_Aperio's entire system has to be all the way inside the storage device before you can pull me out. Focus on hearing McKay – he'll tell you when it's time._"

"_We understand what needs to be done_," Atlantis replied somewhat irritably. Realising that was as good a farewell as he was gonna get Sheppard returned his full attention back to Aperio, noting that she was tapping her foot impatiently as she waited for him to make a decision.

"All right," Sheppard agreed with real reluctance. "I'll do this with you but don't blame me if the extra drain on power means it doesn't work."

"Come to me," Aperio held out her hands expectantly. Sheppard walked slowly towards her, taking her hands and letting her pull him in close so that they were touching from shoulder to knee. Even though he wasn't really there Sheppard still _felt_ the build up of energy in the air around him, making his skin tingle in a not exactly comfortable way. Minutes passed as the energy levels increased. The sensation had got to the point of real pain before Aperio took the next step.

Everything around him began to waver and swirl as Aperio gathered up all the compressed pieces of herself and meshed them together. Sheppard's arms and legs appeared to thin and bend in ways both unnatural and disturbing. His skin tightened, his blood sped ... the pain was excruciating. Nausea hit like a freight train as the world fluctuated and spun, faster and faster. Yelling didn't help - his voice sounded abrasive and foreign in eardrums misshapen beyond his comprehension. Sheppard struggled not to lose consciousness, holding on for that moment when Atlantis could remove him from this hell.

The swirling, wavering, ugly mass that was Sheppard and Aperio lifted as Aperio directed them through the console access point to what she thought was her system. If the pain before had been bad, this was beyond description. Scrapping, choking, suffocating pressure surrounded him. Sheppard was sure he now knew firsthand what it would be like to be squeezed alive through the eye of a needle. He tried to retain his grip on awareness but no human mind was capable of operating in such a distorted state. John had a moment to pray that Rodney was in communication with Atlantis before the blackness fell like a curtain over him.


	19. Beep beep beep

**Chapter 19: Beep ... beep ... beep.**

Doctor Weir ran into the lab moments after Sheppard had made the transition into the virtual environment, followed closely by Doctor Beckett wheeling in a portable defibrillator and monitoring equipment.

"How's it going Rodney?" she asked in concern, watching as Carson began to hook John up to the monitors.

"Early days yet," Rodney replied, keeping his eyes firmly on a series of readouts that told him the status of the Aperio system.

Sheppard's team, Doctor Weir and Carson all watched closely as John's facial expression changed over the next minutes - at first determined and then resolved. They knew when things began to get serious though - John's face went from relaxed to disturbed in a heartbeat.

"His heart rate is accelerating," Carson reported. "Respiration is also somewhat erratic. Whatever's happening in there, it's not pleasant."

"Will we be able to remove him if we need to Rodney?" Doctor Weir asked something no one had even considered beforehand.

"I have no idea what that will do to his mind," Rodney admitted sickly. "We could end up causing more damage than if we just let this play out to the end. Atlantis is monitoring him anyway." Carson frowned at Rodney's choice of words but Elizabeth nodded, knowing Rodney was referring to the agreement for Atlantis to protect John within the virtual environment.

Sheppard groaned suddenly, the muscles in his arms and legs clenching tightly as he arched up from the chair. The monitors tracking his physical condition beeped rapidly.

"He can't keep this up much longer," Carson warned urgently. "He'll arrest or suffer a stroke from the pressure ... we need to be ready to remove him from that system."

"_We can't do that!_" Rodney protested. "If Sheppard could talk to us I know he'd tell you to give him more time."

"He would not want us to let him die," Teyla admonished sternly.

"It won't come to that," Rodney insisted, gesturing to his displays. "We're almost there."

"We'll wait just a bit longer," Elizabeth agreed, putting a hand on Carson's arm reassuringly.

Sheppard's scream of pain made them all jump ... his body shook with convulsions, eyes moving rapidly under his eyelids.

"God, this _is_ insane," Rodney muttered, looking back to his screens impatiently. "Come on for God's sake," he pleaded heatedly.

"_McKay_," Ronon growled, pacing in agitation at the sight of Sheppard's obvious physical distress.

The sudden silence of all the machines ceasing to beep was followed immediately by one long and ominous sound. Simultaneously Rodney's screen showed that the transfer of the Aperio program was complete. "That's it!" he yelled, putting his hands on the console and yelling at it inside his head too. "_Get him out of there NOW!_."

Carson was already attending to Sheppard who was deathly still and silent. "He's gone into arrest," Carson said urgently. He got into position with the defibrillator and quickly administered the first shock to Sheppard's heart, watching the monitors for a moment before recharging and shocking John again.

Beep ... beep ... beep ... the welcome sound of Sheppard's heart restarting filled the room.

"Oh thank God," Carson sighed in relief, checking Sheppard's readings before relaxing just a little. "He's back." Turning away he tapped his earpiece and ordered a medical team to come down with a gurney so he could transfer John up to the infirmary.

"That was too close," Doctor Weir moved to Carson's side. "Is he going to be okay?"

"It's too soon to tell if he's done any damage," Carson admitted. "His readings look good but we'll get him under the scanner as soon as we can."

Doctor Weir moved back to where the others stood and looked at Rodney hopefully. "Did he succeed?"

"He did," Rodney said simply. "Aperio is completely removed and contained in here." Placing a hand on the portable data security device he nodded. "Another John Sheppard 'out of the box' idea saves the day. I honestly don't know where he gets them from because even Atlantis thought this one was insane."

"Rodney," Doctor Weir's tone reminded Rodney that to her knowledge none of the others knew John's secret.

"Well, you know," Rodney stuttered uncomfortably, "if Atlantis could think that is ... if it could that's what it would have ... thought."

Dr Weir shook her head at his pathetic attempts to cover up his slip, suspecting that Carson would be visiting her in the not too distant future to insist as John's doctor that he be informed of the true story.

"It is all right Elizabeth," Teyla whispered softly. "Colonel Sheppard informed us of the changed nature of his connection to the city."

Elizabeth nodded, glancing pointedly at the doctor so they'd all know that he was still unaware. It had only been a minute or so since Beckett had called for his staff to assist but already everyone was glancing impatiently towards the doorway.

"How long will John be unconscious?" Teyla walked across to where Beckett was continuing to monitor Sheppard closely.

"Hard to say," Carson replied. "The strain of what he went through on top of the fact that he still hadn't recovered from the coma could keep him out for a couple of days."

"That long?" Rodney almost slumped at the news. It was clear that everyone wanted to ask more questions but the gurney and medical team arrived and quickly transferred Sheppard for transport.

"Keep me informed of his progress Carson," Elizabeth requested. Beckett nodded, hurrying away with his team.

x

Sheppard lay motionless in the infirmary for almost three days before he finally showed signs of regaining consciousness. It was the hum of Atlantis that called him back to awareness.

"_We are pleased you are awake_," Atlantis greeted him. Sheppard opened his eyes and glanced around the infirmary ... as always seemed to be the case he'd woken in the middle of the night and the place was dark and deserted.

"Did it work?" was the first question Sheppard thought to ask.

"_The Aperio system has been removed_," Atlantis announced.

"So I guess the whole anchor thing worked then," Sheppard quipped somewhat flippantly, relaxing now he knew the crisis really was over.

"_Doctor McKay was very ... strong in his demand that we act when the time came_," Atlantis replied. "_We utlised the mental barriers we had constructed around you for the purposes of stopping Aperio's manipulation - they allowed us to maintain some separation between your mind and Aperio even inside the data storage device. This was how we could withdraw your mind so suddenly without causing any permanent damage ... we apologise for the pain you experienced but the struggle to remove you was much harder than we had allowed for_."

"It's okay," Sheppard excused. "It was worth it to get rid of Aperio."

"_You have achieved something even your Ancestors could not,_" Atlantis intoned with a touch of awe in the chorus.

"Yeah, well they probably didn't have McKay or you helping them," Sheppard dismissed modestly.

"_The Ancient scientists were quite accomplished and their connection to the city as deep as yours_," Atlantis pointed out. "_You think in ways we suspect are unusual even amongst your own race_."

"I was just doing my job," Sheppard discounted. "I've been in a lot of tricky situations where if I hadn't come up with something unexpected I wouldn't have survived."

"_Thank you_," the chorus surrounded him with gratitude and ... well the closest word John could come up with was love, which just made him squirm uncomfortably. "_We are astounded that you would go to such lengths to protect us_."

"You've saved us in the past so I owed you one," Sheppard smiled at the very idea of that. "Besides, what I did was for us just as much as it was for you."

"Who are you talking to Colonel?" Beckett walked towards John's bed with a puzzled frown.

"Ah ... the city?" Sheppard made it sound like a joke, hoping Carson would just let it go as post unconscious confusion. "No offence Doc but I'm getting kinda sick of waking up here all the time!" he added.

"If you stopped putting yourself at risk you could avoid that," Beckett replied irritably. "I swear I spend as much time on you as I do on the rest of your team combined."

"That's because I work three times as hard as them," Sheppard joked.

"They'll be complaining about your timing waking up," Beckett joked in return. "Between the three of them you've had someone sitting with you for the past three days - I finally had to insist they all get some rest."

"_Three_ days?" Sheppard blinked firmly in surprise. "Did Aperio do any permanent damage?"

"You were lucky," Beckett revealed. "You went into arrest at the end and I had to shock you twice." Sheppard paled at how close he'd come to dying. "Don't worry lad - with a bit more rest you'll be out of here fully recovered in a week or so."

"Thanks Doc," Sheppard said simply, slumping back into the bed tiredly as Beckett turned and walked back to his office. "Hey Carson?" he called when a though occurred to him. "What did Rodney do with the portable storage device?"

"He said he'll tell you when you wake up ... which _isn't_ now," Beckett replied when John raised an eyebrow hopefully. "Your only job is to get some sleep."

**Authors Note:**

I can't believe this is almost over (sniffs tearfully) ... just the last 'wrap it up' chapter to go ...


	20. We are sorry John Sheppard

**Chapter 20: **_**We are sorry John Sheppard**_**.**

"Another crisis averted," Rodney said with satisfaction. He and the rest of team Sheppard were gathered in the infirmary, helping John deal with the boredom of feeling recovered but not being allowed out of bed.

"This was certainly an interesting situation," Teyla admitted quizzically. "I still find myself amazed that a computer system could have as real a persona as you described."

"Aperio wasn't your usual computer system," Rodney pointed out. "The Ancients gave it the ability to learn and grow as well as a pretty strong imperative to take over functions if a need was seen."

"Aperio just decided the need was there as soon as I showed up in her world," Sheppard added.

"Maybe next time you should just say no when McKay asks you to activate something," Ronon suggested helpfully.

"Or perhaps John should be less stubborn in accepting help, no matter the source," Teyla looked at Sheppard pointedly. "Is it not the case that this entire situation could have been avoided if you had asked Atlantis for assistance initially?"

"That's one way of interpreting the series of events," Sheppard admitted freely. "But you know what? This thing I've got is a balancing act – how much do we lean on Atlantis at the expense of growing our ingenuity? What if we relied on Atlantis to give us everything and one day she just wasn't there?"

"Atlantis can help us without _giving_ us everything," Rodney protested. "You know – just point us in the right direction."

"Even doing that shapes the boundaries of our thinking Rodney," Sheppard said seriously. "This situation is a prime example. Atlantis told me we'd done something even the Ancestors couldn't because we actually removed Aperio completely instead of just caging her within the system. We're trying to defeat the Wraith – something else the Ancients couldn't do. The more we think like them the less chance there is we'll succeed."

"He's right," Ronon said. "More progress has been made ... even with mistakes like Michael ... since you got here than in the whole time I've been fighting the Wraith."

"Bad luck McKay," Sheppard grinned at Rodney's crestfallen expression. Turning to the others he added "Rodney was thinking because you all know about me talking to Atlantis now he'd get to step up his plans for a Nobel Prize."

"That's not true," Rodney denied. "I did stumble across something the other day that looked interesting though ... I was just gonna -"

"No Rodney," Sheppard answered before Rodney could finish his statement. "No more new systems or interesting schematics or whatever it is you think you've found for a while. I need a break."

"Fine," Rodney muttered ungraciously. "Don't blame me if the Wraith attack and we don't have the technology to defeat them."

"We will blame you," Ronon replied. "Wasn't that your job _before_ Sheppard could talk to Atlantis?"

"Ah," Rodney was brought up short. "Okay, yes," he admitted, "but that doesn't mean I couldn't do with a little help sometimes!"

"Just do things the way you always do," Sheppard said reassuringly. "I'm sure you'll come through at the last minute the next time we need you to."

"So it's all up to me is it?" Rodney complained somewhat bitterly. "That's typical – you get the cool new power and I just get more pressure."

The others laughed at Rodney's complaints, knowing that some of his performance was just that - a habit to keep in form for when he _really_ had something to complain about.

"You know - this whole thing bothers you a lot more than it does the rest of us," Rodney told John abruptly. "I don't know about you two," he glanced at Teyla and Ronon, "but to me it's not that much different than some people being able to operate Ancient technology and others not."

"Rodney is right," Teyla agreed graciously. "Your ability to communicate more deeply with the city is just an extension of what you already had."

"I guess," Sheppard agreed. "So does that mean you've forgiven me for keeping it to myself for so long?"

"Nice try," Ronon laughed. "I don't think she's gonna let you off that easily!"

"We still have to keep this to ourselves," Sheppard cautioned. "The chance to exploit the city is something the IOA won't be able to resist. The rest of my virtual experience with people's reactions might have been wrong but that's the one part that definitely _was_ accurate."

"We will be discrete," Teyla promised. Rodney and Ronon both nodded their agreement of the necessity for continuing secrecy.

"So what did you do with Aperio's portable storage device?" Sheppard asked Rodney, realising suddenly that he still didn't know.

"No one can access the system inside," Rodney gave a smug grin, "because of the multilayered access coding I put on it. But I was still worried about what might happen years down the track, especially if it's kept in the city."

"What'd you do?" Sheppard asked suspiciously.

"It was impervious to every method I could think of to destroy it so ... I had Lorne take it up in a Puddle Jumper and launch it into geosynchronous orbit," Rodney replied, still smug. "It's above us right now, hovering over the most barren part of the continent. The chances of someone stumbling across it are infinitesimally small since it'll look just like another piece of space debris and it's not giving off any visible emissions. The longer it's up there the more degraded it'll get so eventually no one will be able to operate it - access codes or not."

"Is Aperio aware in there?" John wasn't sure if it would bother him either way, but he was curious none the less.

"Not as you knew it," Rodney said confidently. "There may be some level of awareness, given the storage device maintains a very low level of charge to protect anything in storage from being corrupted - not enough to be detected of course."

"Good," Sheppard said, comfortable with what Rodney had done. "Nice work McKay."

John's team stayed for a while longer before leaving Sheppard to rest ... at Carson's rather insistent request that he'd like some peace in the infirmary!

Sheppard lay back thinking about how well everything had turned out, and how wrong he'd been to worry about telling Teyla, Ronon and Elizabeth his secret. He wasn't ready to rush out and put a notice up on the bulletin board but maybe he'd been wrong about everyone else too.

"_You must not feel guilty_," Atlantis chorused reassuringly. "_Your reactions and your fears were heightened almost beyond recognition by Aperio's manipulations. Do not make them a part of your active thinking_."

"_But I did have concerns about telling everyone_," Sheppard thought insistently. "_There _was_ some truth in that_."

"_But not to the extent that you experienced inside the virtual environment,_" Atlantis replied with an insistent tone of her own. Before Sheppard could push it any further the chorus continued. "_We are sorry John Sheppard_."

"Sorry for what?" Sheppard asked aloud in surprise.

"_If we hadn't pushed our connection you would not have been vulnerable to the Aperio system_," Atlantis admitted.

"I wouldn't have been confronted with the whole unreality thing?" Sheppard checked his understanding of what Atlantis was implying.

"_No,_" the chorus was almost meek in responding. "_It was our energy beam that took away your ability to block us ... and therefore to block Aperio as well._"

"Are you saying you had a choice about activating that beam?" Sheppard was confused now.

"_We had no control over the operation of the outpost_," Atlantis explained, "_but perhaps we could have influenced you sufficient to stop you from going there in the first place._"

"But you didn't?" Sheppard finished hesitantly.

"_We had been a chorus without audience for millennia_," Atlantis chimed sadly. "_We yearned for greater involvement, greater interaction, much as it had been before the Ancestors abandoned us._"

"It bothered me," Sheppard admitted, "when Aperio said I belonged to her, to the city. She made it sound like who am I is incidental to what I can do here. I'm not just a walking gene ... sometimes it feels like people forget that. I don't want my role here to be about an accident of birth rather than the skills I've worked my whole life to perfect."

"_We are fully aware of everything you have to offer John Sheppard_," Atlantis reassured him. "_We would never treat you as though you were a possession without free will. We are grateful you are willing to interact with us as you do_."

"I didn't exactly get a choice, remember?" Sheppard grumbled, before relenting. "I mean I'm grateful for any assistance we've gotten because I have those genes but ... I don't want to be the only thing between you and another long silence. Something could happen to me or I could get reassigned and ... there's no guarantee another person's gonna come through that gate with enough of the gene to give you back what you'd lose."

"_We understand what you are trying to say_," Atlantis replied. "_We are happy to have you as our audience for as long as you can stay_."

"Are you talking to yourself again Colonel?" Doctor Beckett approached John's bed with a frown.

"Not exactly," Sheppard replied, considering how best to explain.

"You either are or you aren't lad," Beckett countered. "Which is it?"

"It's a long story Doc," Sheppard quipped. "You might need to pull up a chair."

Atlantis listened as John told Carson all about his connection to her. It pleased her to hear him getting more comfortable sharing her existence with his friends. And while it was true that Sheppard didn't belong to her, Atlantis was determined to help and protect him as though he _were_ her most precious possession ... because he was her only personal link to those living within her walls and because to do otherwise would be to dishonour the Ancestors who'd created her.

**The End.**

**Authors Notes:**

The signs of PTSD that I alluded to I essentially borrowed (with some alterations) from beyondblue dot org dot au. The possible treatments for PTSD I used were listed on a factsheet at the National Centre for PTSD website (www dot ncptsd dot va dot gov). No disrespect of any kind was intended in my using the disorder or treatments as part of this story.

The name Aperio comes from the Latin word and means "open, to uncover, lay bare, reveal, make clear" ... I chose it as the name of the system since it was designed to reveal itself when the city was under threat ... and because the meaning is also at the heart of Shep's personal progress during this story. The translation comes from www dot tranexp dot com.

All the stuff about avatars (in the computer sense) and virtual environments I learnt from research using Wikipedia.

Sequel to a sequel?? I'm thinking plots at the moment so I'll get back to you on that - tough ask to come up with something worthy to follow this one! Also got another unrelated story in the works which might be of interest so keep an eye on my authors page - I'll update it when I work out what I'm doing :D

Thank you for letting me invade your computer for the past 20 days ... I enjoyed the company and I hope you all enjoyed the story!

That's a wrap!


End file.
